First you are asking the wrong question.  By asking what you can do to prove that the fab is bad, you have greatly reduced your chances of finding out what the problem is and fixing it.

It is very rare that fabs would be inconsistent enough for some, but not all, boards to fail paste alignment.

Second, you may have answered your own question.  The same boards are being pasted by two different vendors.  One is failing the other is not.

Pete