I see, but that just makes me want to blame the model even more.
What can happen if you repair a bad model is that intersecting faces are merged in a way that leads to voids on the inside of your model. If that's the case it's really hard to fix for somebody who doesn't have experience with pointcloud based 3d modeling.
Please print something that you know is "good", like the official 3d benchy. I'm almost certain it won't have the holes that you're experiencing on your part.
Edit: do you have a link to the moddel? Then I can confirm for you whether the problem is with the mesh or not.
That's why open source rules