Before you try to subset the font, does the ePub actually pass validation? I ask this because of...
Code:
Decreased the font OEBPS/Fonts/VeraMono.ttf to 57.9% of its original size
The font OEBPS/Fonts/VeraMono.ttf is unused. Removing it.
The font OEBPS/Fonts/VeraMono.ttf is unused. Removing it.
From what I see, Calibre is having a problem because of a problem in your code. Calibre should not be subsetting an unused font. If your code validates, post your CSS and OPF. If it does not validate and once the errors are fixed so it does validate and Calibre still has trouble, then post the CSS and OPF.