@Vansi: as for poin 1) i have faced nearly 10 base crackdowns in a brand new game on 0.99J4 (jack sparrow mode), and gals always spawned in barrack vaults, radar, mess hall and corridors, i never seen them in an hangar. Maybe you update from an opder version, or pheraps just it's bad luck.
I am playing on highest difficulty since April and during 10, maybe 15 base defenses it happened to me 3 or 4 times. Right now I am not updating, 99J3 IMO breaks economy too much. I'll update when Reticulans show up and sectoweed will be buyable.
As for point 3) i never saw it, and i play this mod on and off for about 2 years, maybe again a problematic update or a map problem? More likely the second, but I'd try to reinstall it, i've done it sometimes since i had more than once corrupted installations
Outside mission "Raynerd must survive" I saw it only once and it is on that screenshot in my post above. But during mission "Raynerd must survive" terrain bugs I described are common and as soon as I get that mission again (or savegame with it) I'll take screenshots.
More bugs (game ver. 99J2):
1. FUBAR numbers in ranged combat chance to hit. You can have chance to hit over 200% and still miss. Twice. If you are using Custom Sniping Rifle. Very rare, but happens. Misses with CTH over 100% are little bit common.
2. FUBAR numbers in melee combat chance to hit. 100% CTH gives you in reality 20-30% of hits. CTH 60-70% gives you real CTH maybe 5%, and you can literally miss 15 times in row.
3. Gals are unable to rotate during melee reaction fire. If they don't face enemy perfectly then there is no reaction fire. Even rotating 45 degrees is too much.
4. You can't transfer Alliance Advisors between your bases. There is error message that at target base there is no animal cages. But you can transfer Attack Dogs, White Rabbits or Tamed Werewolfs. Or you can go to the target base and buy Advisor from Black Market.
5. Option "Smooth Bullet Camera" doesn't always work, especially when target is at the edge of the screen or right beyond (I am not talking about edge of the map).