Hi schnoidl,
If I get your question correctly since your question leaves out all the details, you have imported a VDB sequence via VDB Loader and used the Volume Surface object to get polygons. If you used a 3rd party plugin for that, please check with the tech support/forum.
Export your setup as an OBJ sequence (animated). Then reload it. There you get no option to delete a little polygon artifact. That is your question, correct?
Check your sequence, and note the frames you like to work on.
Switch off the Instance. Then twirl opens the hierarchy and sets the Display Tag so all your objects of that sequence become visible.
The top object in that hierarchy to not visible (two red dots, Object Manager).
Each frame you like to work on set to be visible (two green Dots, Object Manager)
Create your changes.
All the best