Mags loaded to full capacity are under very high spring tension, and can vary slightly in how much remaining "slack space" they have. When you insert a mag with the bolt closed, the bolt contacts the stack of ammo in the mag and that ammo has to be pushed further down into the mag. This is why GIs are taught to SMACK the bottom of the mag to ensure it seats properly. You can also underload the mag by a round to two to make tactical reloads easier. Otherwise, just leave the bolt back when loading.
Oh, also, plastic mags often are just slightly too narrow at the feedlips to seat with the bolt forward. After a few uses, the bolt will have shaved just enough material from the feedlips that this will no longer be a problem.
-Troy