The challenge with wheelchairs, particularly the motorised wheelchairs, is their bulk. You can't load them too early and load bags on top or around them as this would cause damage. Bags move in flight and damage can be caused due to in flight turbulence dislodging what had seemed to be securely packed belongings.
On narrow body bulk loaded flights stowage of wheelchairs can be a challenge. Short turn round times result in more haste required to unload/load, and potentially less time to rejig baggage to safeguard wheelchairs. Plus as already mentioned the wheelchairs often arrive at the gate quite late, and if boarding by jet bridge you then have to get the wheelchair down to the ramp via very basic engineering steps on the side of the jet bridge. Not so bad for a pusher wheelchair, but very difficult for a heavy powered wheelchair. It is definitely an area that requires more thought when planning new airports.
With containerised baggage there is more chance, but no guarantee, to have a dedicated bin for the wheelchair(s) and this should reduce the opportunity for damage significantly.
I'm not sure the problem is at epidemic levels, but every time a problem occurs it is maximum disruption for the owner, so in this situation it really does need an effort to drive down to zero the times it happens.