This falls under the "no 2 cars were created equal" rule. My buddies car is doing the same thing. It seems most all of them go in fine, but every once in a while someone has problems. I have found that the stock frame pad/towers that are bolted to the crossmember to be the cause. If they were formed slightly differently, the corners will be sharper, and they will interfere with the welds on the new poly mounts.
Check to see where they are hitting first. You may have to grind the corners so they are more rounded on the frame pad/towers. Once you eliminate this interference, that usually fixes things. If it still does not fit up, then you can loosen the bolts to the block & adjust. You can try fitting it up with these slightly loose, but if it is too far off it will not bolt up right. I would just loosen the bolts & make sure the mounts are down against the bolts before tightening. There is a little clearance there that can be shifted to the downside. If you installed them with the motor upside down, the weight of the mount would have placed them higher when the motor is upright. That would throw the angles off a bit, but minor amount. As stated above, no 2 cars being the same, your frame pad/towers may have been bolted on slightly differently than most others. You can loosen those bolts & shift the towers around a little to line things up.
All else fails, we are working on an update for them that might make them fit your car a little better. Please DO NOT hog the holes out to fit unless you plan on keeping them whether they work or not. This basically ruins them. If you can't get anything to work out, I can swap you a newer version for those, as long as they have NOT been modified.
PS- PLEASE contact the manufacturer when you (or anyone) has a problem with a product. Some of them may not help you, but we will go out of our way to make sure our customers stay happy. Some other vendor/manufacturers help to various degrees, but at least give them a chance to help fix things. Many times you won't be the first one that experienced the problem, so we may have a fix figured out (like above). Anyway, let me know if you get them to fit up, need more help, or want to swap them out. We will be at Morrocco & bristol if that helps too.