For starters the characters themselves make it non-canon. Maverick, Angel and Maniac...at the very least Maverick and Maniac aren't supposed to be there. Then you have fighter types that aren't put into service for a long time, and all that "spacecraft falling down from the hangar deck into space" crapola....
Better just forget about it
At first I didn't liked the movie myself, because it had so many things changed (desing, backstory for blair, and so on), but after reading StarSoldier manual, and reading a lot of posts done in the general forums about the movie, I started looking at the movie in a different way. It still has some innacuracies that are not explained very well (bossman for instance), but the fans of Wing Commander really try making it canon.
That's something I really like about the Wing Commander fans over the Ultima fans (I'm more of an Ultima fan myself). Instead of saying how bad something is, most of them try to explain things and make it canon, and StarSoldir even made it official. So personally, Standoff did a great thing with Episode 5 intro.