does this happen to any one else?
go to the options, then click on the document properties tab at the top, then click on Detailing.
There will be a box that shows the Display Filter. Click on Cosmetic Threads. That should turn it off.
another option is, do you have the sketch being shown? Use the Hide/Show items bar to turn on/off planes, sketches, points, etc...
just throwing things out there.
When you are in the Hole Specification's menu under options select the button I have circled in the image below.
This will get rid of the the dashed lines which are just a representation of a tapped hole. On a flat part the are on the surface you select, but I'm guessing you made this tapped hole based off of a plane and extruded out far enough to penetrate you tube, therefore the dashed lines are on the inside of your tube.