(Or seen this with any other GB.) Have they seen a similar situation!
Yes, happens all the time.
To check this, go look at some GBs you've never built that you have collected a lot of BPs for.
Atomium is the second GB listed in my Inventory. I have a total of 219 BPs. average is 23 per slot. Left to right, top to bottom individually 27, 30, 14, 28, 29, 27, 24, 20, 30
No statistical anomalies there.
IIf I built it through lvl 23 (That would take 14 sets od BPs.), I'd have 105 BPs left over, average 11 per slot.
Individually though they'd be left to right, top to botto, 13, 16, 0, 14, 16, 13, 10, 6, 16
That 0 sticks out. And yet the total number of BPs never changed.