If you’ve had a claim rejected, you should examine the arguments that HMRC lays out in their correspondence. Often, there will be counterarguments or additional evidence that you can present in response. HMRC is not always so precise in their investigation, and they may even ask questions which you have already answered in the initial claim.
Another good option is to have a trusted colleague or professional connection, particularly someone with experience in R&D tax relief, look over the claim. With so much depth and complexity to the scheme, having other experiences that you can draw on is a big strength. Here are some resources that you can use to strengthen your claims process: