Removing the door is fine if most of the model is in the ground. However, the helicopter shouldn't be causing collision glitches. What's most likely happening is that the model is just clipping with the map. I can remove that one as well though.
Also, thanks for bringing this up El Flaco. It's always nice to see people bringing up problems they have on the forum so that we can be aware of it. That way we can have a discussion about it as a community.