Library showing new changes to be published, immediately after publishing changes

We have twice recently found Figma saying that there are new changes that have been made to our file and need to be published immediately after publishing changes. The new changes have no direct relation to the previous publish, and no branch merges or edits have happened since the publish. Forced to publish new changes, but after the next publish no updates to said items appear in the accept from main popup. Have tried closing, restarting, rebooting with both Mac app and online versions and nothing seems to help. Anyone else having this issue?