Due to a bug in Illustrator when dealing with compound paths, you might end up importing incomplete shapes, missing parts or weird overlaps in Fontself that can appear as white lines / borders in your shapes for example.
In such case, clean up your vector shapes:
First, try using the command Object > Flatten Transparency with default settings to clean up a shape.
Else try boolean operations: start by applying the Pathfinder > Unite feature in Illustrator to merge all the shapes for a single character (you should turn on the Remove Redundant Points option in the Pathfinder's options menu to clean up extra points).
And if you have stroked-only letter with counter-forms, and want to avoid outlining strokes, try Compound Path > Release instead (make sure that all parts of each glyph are still grouped as a single object before importing in Fontself).
In most cases, you should then be able to import your glyphs properly. If not, send us your .ai source file to email@example.com and we will have a look.