This tendency is a classic case of the genius of embracing constraint - a tendency that, in other media, leads to classic design. In an analogous experience, consider the MRI in House. Generally speaking, entering the MRI machine in Princeton Plainsboro Hospital is a disastrous experience. Why? Because an MRI is a fairly standard medical procedure, and thus tends to occur early in the episode, but due to the nature of television, diagnosis is only possible in the last five minutes of an episode. Accordingly, all diagnostic techniques early in the episode are necessarily disastrous - thus the MRI, which is always going to be towards the beginning - never works. And from this comes a fundamental piece of the lore of the show.
Similarly, take Elevator Action - a minor classic of the classic arcade game era. Your avatar is a spy seeking to steal secret plans from a building full of black-hatted men with laser pistols and escape out the basement. The major way in which you handle the endless swarm of black-hatted men is to cleverly use elevators to evade them. At the top of the building this is straightforward - a single shaft drops down the center of the building. But as you descend, the pattern of elevators becomes more complex - not all elevators serve all floors, and attention must be split between navigating the building's eccentricities and shooting people.
These floors are where the meat of the game is, and it's a pleasant meat in the classic arcade style. The game, in essence, is about the fabulously bad architecture of the building itself. Understood psychogeographically, a building is a container for lived human experience connected to other containers through an indirectly-causal network constituting a larger container for lived human experience. Or, to put it another way, buildings are where stuff happens. They are thus understandable as media themselves. The classroom building I walk into three days a week is designed to produce classes in an almost industrialized way - uniform, interchangable classrooms, each designed as theaters-in-miniature, thus privileging a particular educational style. Much of this privileging occurs through old decisions - an investment in a particular type of student desk that creates a particular classroom setup, an investment in chalkboards that is anachronistic given their failure to play well with computers, etc.
The building of Elevator Action, bizarrely, is actually designed for being infiltrated from the top down by someone being chased by an endless legion of black-hatted men with laser pistols. Which, from an urban development perspective has to be considered an odd decision that would be a tough sell even in Dynatron City. Which is typically video game, really - the odd, monstrous object that is itself a parallel to the monstrosity inherent in the medium. The building in Elevator Action does not function sanely precisely because it is designed to be part of a difficult-to-control video game.
Or there is Eliminator Boat Duel. Slotting as it does squarely into the long and storied tradition of racing video games, it continues the theme of erratic machines perfectly. Racing games are infamous for a particular mode of artificial intelligence called rubberbanding. In this mode, the skill of computer players is set automatically and dynamically at whatever will pose a suitable challenge. Thus in a racing game if you are doing appallingly badly, computer vehicles will be pegged to go slower so you have a chance of catching back up, whereas if you are doing extremely well, computer vehicles will be sped up to be right on your heels no matter how well you do.
This is a different sort of erratic device, but still fits firmly into the tradition - a device in game that behaves with odd inconsistency but is nevertheless the main thing you have to control and interact with. In this case, however, the device gives the illusion of normal function, as its eccentricities exist because it works in what is functionally a completely different world from the other vehicles. It is impossible to meaningfully describe rubberbanding except in terms of the subjectivity of a given vehicle. That is, it is impossible to definitively state whether the player's vehicle is slowed down if it gets too far ahead or whether opponent vehicles are sped up if they get too far behind.
This is because a racing game has an ambiguous sense of setting. Ostensibly it takes place on a defined track of land. But in reality, a race course is defined via a spatial coherence that is only possible in real space. There is no such thing as a meter in a video game. There is no such thing as any length, in fact, except as determined in relation to another physical object.
At the core of it, of course, this is true for real world measurements - a meter was defined in 1790 in terms of a pendulum, and has gone through several more definitions before reaching its current definition as the distance traversed by light in a vacuum in 1/299792458 of a second. The kilogram, on the other hand, is to this day defined as being equal to a lump of a platinum-iridium alloy sitting in a vault in France. Notably, this cylinder of metal is known to have changed slightly in weight, meaning the definition of a kilogram is in fact always in slight flux. I am, however, unaware of any game that implements anything remotely similar to the kilogram to create a standardized unit of measurement in game. As a result, any measurement is not a reference to an essentially arbitrary absolute, but comparative. At best measurement can be conducted in pixels, but this only works for games with no use of perspectival representation at all.
So a game such as Eliminator Boat Duel is bizarrely arbitrary - two boats race around a track of indeterminate size in mutually contradictory time scales. Such that the track cannot be said to meaningfully contain boats at any point along it, and no boat can meaningfully describe its relationship to any other boat because they are moving through non-space not only at differing speeds, but with differing conceptions of what speed is. The closest thing to a coherent description the game offers is the news that damaged boats go slower. But what damage means is esoteric in this context. Damage is something that impairs normal function - but a boat's job is to traverse water, and given that water, space, and motion are fungible concepts, impairment seems equally obscure.
What is most striking about this is not its eccentricity, but its normality. None of this makes the game even remotely difficult to understand or to play. And Eliminator Boat Duel is actually considerably less strange than some video games - consider, for example, that Hyrule, in the first Zelda game, appears to have an obsession with a measurement that is not only the exact height of a normal human being, but also the size of every single rock, weapon, and indigenous lifeform save a handful of boss monsters.
No. This confused space is not extraneous to video games, nor is it a problem. It is what video games are - temperamental and eccentric machinery.