Is there a plothole in Merlin's character development?
Okay, so basically thanks to fellow Redditors, that sounds like a little plothole. The main reasons expressed there are:


It is not an immunity, it is an ability to nullify Commandments.
She forgot that she had this protection on her (the blessing happened 3000 years prior to the main story), which explains why she still suffered the effect.


As for "Is it a valid reason to explain something that should have not happened", it is an open question on which everyone might have his opinion.