I'd be interested if you expounded on the problems. Some parts of the movie are confusing, but I never know if it's just because I'm not getting it, or because of problems with the story line. Overall, I'm amazed at how technically sound much of it is.
OK, here's a brief list of my problems with "2001":
1. The timeline was absurdly optimistic. Understandable given the level of spending on space exploration in the mid 1960s.
2. Totally missed the digital revolution. There are flat panel displays all over, but the cameras use analog film. When they pose for a pic with the monolith on the moon, the photographer has to keep winding the film. During the intermission at the screening Monday, everyone pulled supercomputers out of their pockets and checked social media. Computers in "2001" are still big, bulky, centralized things.
3. Gender roles haven't budged. Every pilot is a man. Every flight attendant is a woman. There are a couple of lady Russian scientists, but everyone else is a dude.
4. Everyone tries to walk in low or no gravity. They have sticky shoes. No one really does that.
5. Humans are special because they use tools. We now know lots of other animals use tools. Some even fashion them. The Dawn of Man monkeys don't even fashion their tools, they just bust heads with bones they find laying around.
6. The big one: the film is deeply anti-scientific. It is rooted in a pre-scientific dualism that cannot fully accept evolution. Evolution can make timid shrub eating monkeys, but some external force has to impart the Spark of Specialness before we make the leap from ape to man. Nevermind that the monoliths just kick the can of consciousness down the road a bit (where did the monolith creators get their Spark?). "2001" perpetuates a dangerous, outmoded way of thinking about humans that keeps them distinct, special and above the rest of "nature".