I have a similar issue:
Signed this striker in the League Two. Was able to assign him an ESC spot. After getting promoted, I extended his contract, had to go through the WP stuff again, and got this screen (this is the second appeal). After clicking allocate ESC Place, the player won't be assigned an ESC place and is ineligible to appear in games.
Now after waiting for a second appeal for a WP, this happened again
I have a Save File ready to share if this is needed.