In some cases you need to remove tension from your derailleur. I know I have a bike where everything fits just fine and no issues with the axle or frame but because the clutch is adding extra tension it will not allow the thru-axle to thread in properly. Luckily that particular bike I am mentioning has the ability to lock the derailleur into a different position for situations like this. You might be having a similar issue but have different parts which are less likely to have that issues in the same way.

If the hub fits in the frame without stretching and the thru-axle fits properly without the wheel then try to loosen tension on the derailleur.