Welcome to Knitting Help!
Gussets can be a problem for a lot of things. You might try intentionally twisting the stitch by knitting through the back loop of the stitch (or front loop if that twists it). If you need to you can also pick up an extra stitch and then on the next row knit those two together.
If all else fails you can use some yarn to weave in around them, kind of duplicates stitching, when you're all done.