Well....on the mothership, I'm thinking you're shooting in the black area around it. Shots look like they'll go through it, but they won't.
Phoenix in newer MAME is just harder. I'd have to sit down and compare, but it may just be that the baddies are more devious.
However, just now I got juked in two consecutive games, where I pushed my shield, and it activated AFTER I got hit. ? Then twice where I'm pretty sure I got bombed, pressed my shield, and there were some rounds left after it died, but I was now just to the side of that spot - and I died! I'm wondering whether MAME is accurate, and if it is, it's as ---fouled up beyond all recognition--- up as the game was originally. I don't remember as I only played this a few times as a kid, and didn't like it anyways.