I just started A08: Wrong Side and right at the start there is a conscript on the bridge. My SEALs outright refuse to attack it. When I give an attack order they swim for the closest shore which is protected by two tesla coils.
I looked in the playthrough on youtube and there the SEALs do attack the conscript, but mine are simply not doing that.
I think SEALs have been balanced since then and are incapable of attacking that conscript, you just have to swim past him and bait the subs out of his range.. usually best to destroy them after clearing the beach as a result.