Sounds like a conflict....unable to fill a compartment because the area is damaged/destroyed. Being able to put enabled men in does puzzle me though
There are one or two other quirks that have evaded modding attempts with no rational reason being uncovered (no point in highlighting them here if still undiscovered).
Like the above I presume the fault was miraculously sorted on the next patrol.
The 'labotomy' bit must be a 'no brainer' though