The book 2001: The Lost Science, which is filled with diagrams and notes from Frederick I. Ordway III (the main science consultant for the movie), says on page 41 that the Discovery has an internal centrifuge which spins to create artificial gravity, without the whole ship needing to spin with it. Then it says on p. 56 that they had a choice of different possible ways it could spin, either constant low-gravity or short periods of higher gravity (not clear what this choice was based on, my first guess was something to do with energy requirements, and @uhoh also had a good speculation in a comment that they were thinking in terms of total 'g-hours' needed to maintain a healthy body). They opted for a constant low-gravity spin, but they realized the set was a bit too small for what would be needed to avoid problems with the Coriolis force that would be experienced when moving around inside the centrifuge:
We had the option of putting the Centrifuge on for, say, one to two hours a day to produce up to 1.5 g, or permanently have it rotate to provide about 0.2 to 0.3 g. We chose the latter. There was, of course, the problem of Coriolis forces, which on small diameter wheels would cause dizziness to astronauts walking along the rim. Calculations showed that a centrifuge should be at least 300 ft in diameter to reduce to acceptable levels the inconveniences caused by the Coriolis forces, but such a diameter was beyond the capabilities of the M-G-M British Studios — and our budget. So we never really mentioned the diameter of the wheel with which we had to work; in fact, there was no purpose to reveal the measurements at any time. Visual appearances were what counted.
The introduction to the book says "A significant portion of the background text presented in the following pages was written by Fred Ordway at the time of production", and the phrasing in the excerpt above ('We had the option') would suggest it's one of the parts that was written by Ordway.
So, the short answer is that in their heads the centrifuge was meant to have a diameter of about 300 feet, but they couldn't get a set that big for budget reasons, so they just used a little visual artistic license. An article here says that based on visual appearances, it looks like the centrifuge set used in the film actually has a radius of at most about 8 meters (which would be a diameter of 53 feet), and @Organic Marble mentioned in a comment that the book The Making of Kubrick's 2001 by Jerome Agel said that the set was actually about 38 feet in diameter.