I have had that issue before. What I have found works for me is the increase density (make it darker) when you print it out. Also, make sure the board is sanded smooth. There have been times I figured I would just put the pattern on the board because it seemed smooth enough. That is not always the case. I use a small orbital sander with about 400 grit sandpaper. Does not required a lot of effort, 4 or 5 passes will do. Clean it off once sanded, vacuum or brush. Then apply the pattern.
Also, I have had to learn patience. Be sure to let the transfer tool warm up a few minutes. I usually plug mine in and then affix my pattern. It should be hot enough to apply without any issues. I have learned this one the hard way because I wanted the pattern on it right now 🙂
Good luck!
David