I had decided to go to the Murk Forest Hidden Grotto to try to find Delta Scraggy. Sadly, my result was a Chimchar. After killing it, I went to the Hidden Grotto on Route 4 to try to find Delta Sunkern. For some reason, there was no sprite. I walked over to and interacted with where it would be and I got an encounter. Surprise: Chimchar showed up again. According to the wiki, Chimchar should not appear there, so I think it has to do with my encounter with it in the Murk Forest.
For testing purposes, I killed it again, then went to the one on Route 3. To be honest, I half expected to find another spriteless Chimchar. Instead I got a Charmander (with its sprite). For my final test, I went to the Hidden Grotto at Midna Garden. The result was a Durant (also with its sprite).
I would guess that this is either A) A problem between the Murk Forest grotto and the Route 4 grotto, B) A problem with the Route 4 grotto that duplicates what you got at the last grotto without its sprite, or C) A problem with the Murk Forest grotto that duplicates what you got there at the next grotto without its sprite.
Option A doesn't seem to be very likely, but I can't test either it or C as that was my only file with access to Murk Forest. In an attempt to test B, however, I went to another file and went to the Route 3 grotto again. The Pokemon I got was a Pansage. After that, I went to the Route 4 grotto. Instead of a Pansage without a sprite, however, I got an Awakening. This leads me to believe that the Option C is the most likely scenario.
(My apologies for the long bug report. I wanted to share the results of my testing to help lessen your workload.)