If you don't have a Vitapod and you pick up a Crystal (without having one already), it acts as a +2 Vitapod.
General Bug - Crystals
At first, I was confused with the term "Crystals" - I realized you meant minerals then it all made sense.
I'll use an example - My armor is currently Cobalt (helm/armor both). Before hitting level 5 (aka no health bonus), I would start each gate (mission or normal) with 5 bars. When I picked up a mineral, I'd get 2 empty bars added. (This was without respect to the size of the mineral). Then, if I picked up a +1 vitapod, I'd have 8 bars of health - with no armor bonus. Once the cobalt hit L5, I had the same bug (except with all numbers 2 higher, starting at 7, had 10 with a single +1 vitapod). I haven't gotten cobalt to L10 to test that yet.
EDIT: Update - I get the +2 the first time I collect anything within a level, including crowns or heat.
It doesn't act like a vitapod, it updates your health to the amount it should be for that depth. The mission center is T1, so you end up starting the missions with T1 health until updated.
I just did a run in Whipping and Mishandling in Proto armor and helm. The minerals don't give any extra health bars.
It's the T1 health bonus limiter bug.
Are you already wearing a higher-tier set which gives health bonuses?
If so, it's the bug with the mission levels.