Nested Brainf*ck loops can be used like this:

+++[>++++[>+++++<-]<-]>>++++++.++++.
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Which in this case is only a fancy way of writting

++++++[>+++++++++++<-]>.++++.
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Both of these should print "BF".

On a closer look at your code I think nested loops are indeed supported however I am having trouble with installing Filter::Simple so I cannot check.

Regarding comments and ` operator: to my understanding anything that is not a Brainf*ck operator (that is not in the []-+,.<> set) is automatically treated as a comment and is silently ignored (this lets you have Brainf*ck code span a couple lines rather than being on one long line). Of course the philosophy should say that Brainf*ck code should not be commented at all because if it was difficult to write it must be difficult to read ;)