Corrupt File, is it possible?

So, I am relatively new to CAM and CNC world. I have been having a blast learning and making things. However, I have been having one hellava time developing detailed coasters that incorporate 5 different tool bits. It seems like every time I either load up the program. Initialise and set Zero, the first pass goes right through my project (walnut). I will delete the program resave the same file and run the programme and it will work.
The newest issue is with the same file but a part of the design is miss aligned with the rest of the paths. I went back to my file and checked the preview to ensure there wasn’t something I missed, and there wasn’t. Tool path that gave me the issue is a 30d VBit (Depth: .0013, Feed: 40, 24000 rpm) I’m not too sure if this would have given me issues.

Is it possible that the file gets corrupted after saving it a bunch of times? I zero my projects to the bottom right of the waste board and zero to the same surface. I use the same “zero” for multiple different projects across different days and turn off my machine in between. Would this be a good practice or be giving me these sorts of errors?

VCarve Pro, Shapeoko Pro is what I’m running. Thank you in advance.

Check the file for where you are setting z zero. Top or bottom.

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I’m setting it at bottom of the piece (top of the wasteboard). I think I figured it out, I had adjusted my feed down to 32 ipm and just made three with no issues as far as the misalignment is concerned.

But as far as my bit punching through my main piece I’m not too sure what is going on.

Update:
The photos below are an example of tonight’s issue. (Mind the burn marks, I’m still learning). The bit looks like it just ran away (right side of the photo). I’m in my shop watching and the machine would run at a constant feed rate then out of nowhere it would take off and get buried into the wood and push through across the piece.

What the design was suppose to look like:

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