Medical needles are probably too thin for the viscosity of glue.
To prevent that in the future, make small cuts on the edge where you fold the vinyl over.
I uploaded some pictures of a little gauge pod I just applied vinyl too. They are high-resolution, so instead of posting them here I'll just post links. They are 6MB, so it will take a bit to download, but should help you see what I mean.
Back
Front
Notice around the corners I made small cuts to allow the vinyl to sit flat where it folds over. On the front of the pod, for the gray piping, I made a bunch of triangle cuts. This helps the vinyl go over the geometry and lets the air out. If you look on the other side, you can see some bumps and so forth, but its fairly flat. Without the little cuts, it would be impossible to upholster to that shape without it having some aesthetic issues.
For long runs, I will make some intermediate cuts also, because if the vinyl isn't cut perfectly straight it will tend to 'buckle' and that makes those little air pockets
Hope that helps.