Hi Spencer!
Are you able to provide some details on what version of ArcGIS Pro you are running and if its an enterprise system? Also are you creating annotations within Pro using label to annotations? Are they stored annotation layers in the database or annotations within a map? Are you importing annotations from another file type (eg CAD)?
ArcGIS Pro changed the way it stores annotations somewhere around Pro 2.0. Annotation layers stored in a database are now stored as point features rather than traditional annotation type layers. This caused issues for me in the past, as I was attempting to run FME workbenches from an older geodatabase to a new one and it was failing repeatedly. I had to convert all annotations to point features before migrating.
You can still import, view and interact annotations from older versions but they can cause issues in Pro.
Theres a tool in the toolbox called 'Upgrade Dataset' which can be used for annotation layers and it'll help get rid of any funny business based on versioning. This can only be run on annotations that are stored as annotation layers in the database, and your database has to be at the right version to support the upgrade also.
My recommendation would be to try to run that tool on all your annotation layers and see if that helps at all.
Let me know if any of this was helpful.
All the best!
Angela