Actually Armadillo has most of its bugs from BB2. Or maybe not bugs but some not quite clear decisions. But I think modifications to it were postponed for later builds, as it is still working even with those issues.
If they exclude the Armadillo from alien bases, which is I think the plan, hopefully you’ll get given a warning that you are deploying with a vehicle that won’t be able to be used in mission and will be given the chance to send different units.
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OK that will explain it. I guess if you can’t use the Armadillo in the Alien bases it will never be a problem getting in it! 
I will miss the meat shield in those corridor caves though haha
My Armadillo cannot reload between missions. It now starts a mission without any ammunition at all!
Sometimes it doesn’t reload between missions. Same with the Scarab.