The pod is a goof -- or not, depending on who you ask. There was an excellent book published around the time the film first came out called "The Odyssey File" which contained early email correspondence between Peter Hyams (writer/director) and Arthur C. Clarke (author of 2010). Hyams asked Clarke a lot of questions about continuity and the like. The issue comes that the novel and film of 2001 are substantially different in certain sequences (for instance, how HAL tries to kill Dave), which results in some discrepancies. Essentially, Clarke told Hyams to go with whatever made the best movie, and if there were minor continuity errors, so be it.
That said, here's the pod situation as best I can figure it out.
Pod 1 (the left pod) was taken out of the ship (offscreen) by Poole; when HAL kills Poole, this pod drifts into space, and we're led to believe that it's lost. I suppose in theory Dave could have gone after it later, but I think it's pretty clear that that pod is gone.
Pod 2 (the center pod) was taken out of the ship (onscreen) by Bowman to retrieve Poole. When HAL locks Bowman out, Bowman uses the emergency airlock to re-enter Discovery. The explosive bolts blow the door to the pod, although we're never show exactly what happens next. I always assumed that pod was lost; presumably the door was floating in space in one direction, the pod itself in another, and who knows if Bowman had the ability to retrieve and repair the pod. I always assumed the second pod was lost after Bowman's re-entrance to Discovery.
The third pod... here's where there's a little bit of a continuity issue. We're shown that the left and center pods have been taken out and most likely lost in space, so there should be one pod remaining - the one to the right (from inside the pod bay -- from the outside of the ship, this would be the left). However, when we see Bowman leave Discovery for the last time, the pod comes out of the center door in the pod bay. There should have been only one pod remaining, the final pod, and that should have been the one that Bowman took on his final journey.
So it's up to the viewer to decide if Bowman retrieved the center pod and re-used it when he left the ship for the last time, or if it was a continuity error on Kubrick's part.
In terms of 2010, the pod being in the Discovery bay is both correct and incorrect, depending on how you want to look at it. In terms of being the sequel to the film, there shouldn't have been any pod in the pod bay, as Bowman should have used them all. Taking into account the possible continuity error in the first film, if there was a pod remaining at all, it should have been the right pod, and not the center one we're shown. HOWEVER, in the novel 2001, when Poole is killed outside the ship, Bowman doesn't go after him. So one pod is lost by Poole, and two remain. Bowman takes one of the remaining pods when he leaves Discovery for the last time, thus leaving one pod left in the pod bay.
In the novel 2010, the use of the extra pod in Discovery became a minor plot point, which is why I'm assuming Clarke decided to keep it in the book. (In most of the other areas where book and film of 2001 were different, in the 2010 novel Clarke for the most part went with the film's version of events rather than the novel's.) The pod doesn't actually serve a plot purpose in the film of 2010, so it didn't "need" to be there.
I was hoping someday I'd have a chance to recycle all of that useless information!