MSA programs make mistakes. Even if no mistakes are made and output MSA is "optimal", we could still be looking at something Biologically meaningless (e.g. the input contains divergent sequences - evolutionary between input the sequences has been completely wiped-out by mutations because those genes were under different evolutionary pressure).
There seems to be 10 or so publications on automated MSA quality scoring.
EDIT (6 month later): Looks like I was wrong, it's not ~10 but ~4 unsupervised methods out there: norMD, Gblocks, HoT, and GUIDANCE. There is also PSAR that claims to be better than GUIDANCE but they only did testing on DNA sequences. And only a few MSA aligners report sites-specific confidence: SOAP, T-COFFEE, FSA.
Does anyone have experience on how these methods perform in practice?