I'm trying to reproduce the error. I'm wondering whether something have changed after you've shared the project. Could you please share the numbers you have used for
1. Depth per pass (was it 0.0028in?)
2. Cut depth (was it 0.0039in?)
3. If you have changed following,
i) Step Over (was it 40%?)
ii) Safety Height (was it 0.15in?)
Also, in successive "generate toolpaths" clicks, did those erroneous lines change, even without changing anything (e.g. above parameters, or any changes to shapes)?
Thank you for helping us to narrow it down.