Hi @starrven0m the only time this has happened to me in the past was when I’d mistakenly left the setting to “stop printing at height (NN)mm”, I know you’ve said it seems to have printed to the appropriate height, but with only 3 layers, at a low layer height, it could be difficult to measure. Three layers is also quite a low number, I typically print so that my solid layers are around 0.8mm - 1.0mm thick (depending upon the purpose/model), so unless you’re printing at 300 microns, it may simply be that you don’t have enough solid layers, especially if your infill percentage is low causing the first couple to “sag” into the infill. Is there any difference in the printing behaviour when it reaches these layers (does the head move obviously more slowly, etc.)?
Some more details (layer height, infill, etc.) and a photo or two would help with diagnosis.