I was having this issue, and I discovered that going into the controls for that particular station (you get there by clicking on that station in the station list) and changing things like minimum/maximum load times and selecting "do not block station" have helped with these issues. For a station that doesn't draw many riders, this prevents empty cars from piling up there and waiting for guests that don't show up (so guests at a busier station aren't piling up waiting for cars to come to theirs). And if a station is completely unused, because that part of the zoo is still not developed, it can help just to keep it turned off.
I also always put the entrances and exits on the opposite sides of the station, or if both left or right entry/exit, to have the exit down a ways from the entrance so the guests are exiting away from where new guests board. Seems to prevent the stuck guests thing.
If this isn't helping, though, I'm not sure what the issue might be.