I have been noticing this for a while now and finally tracked down where it is happening. I reset to factory and changed 1 thing at a time until the problem cropped up. If the first layer is set to 100 then it happens. Any other setting then it is fine. Even 99. It will also fill in over a hole.
The model is fine, remember the layers are good if set to default settings where the first layer is 90
See attachments.