You can't have an anonymous system that simultaneously allows meaningful verification: if there is no way to tie me to my vote in the system, then there is no way for me to prove that my vote was misrepresented to anyone but myself. Even if there were, there is no way for me to prove that my claim about my vote is correct. Even if many people come out claiming that their votes are mis-represented, there is no way to know whether that is a sign of errors/tampering with the system, or a concerted campaign to try to put the election in doubt.

Any system which foregoes physical proof of voting as a base for the count, relying instead on after-the-fact verification, is open to this problem. A complex system, whether software or even mechanical, can never match this level of confidence.