Looking at the Layers view in Cura, the holes were filled all the way up. Unchecking the "fix horrible" settings in expert view seems to have fixed it! Thanks!
I am running another short print but will update here when I try this one again later today.
Please show in slice view or show actual part. I'm going to guess you simply need to turn off "brim".
Or are the filled in all the way up? Try unchecking all the "fix horrible" settings in expert settings.
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