No, you got the error saying that $filename.fa is uninitialized. So perl saw that as a variable name ...

Sorry, but that's not correct in this case, a dot does end the variable name being interpolated. As the OP is using strict, that would have caught the error anyway. Your advice does apply for other characters though.

$ perl -wMstrict -le 'my $fn="x"; print "$fn.y"'
x.y
$ perl -wMstrict -le 'my $fn="x"; print "$fn_y"'
Global symbol "$fn_y" requires explicit package name (did you forget t
+o declare "my $fn_y"?) at -e line 1.
Execution of -e aborted due to compilation errors.
$ perl -w        -le 'my $fn="x"; print "$fn_y"'
Name "main::fn_y" used only once: possible typo at -e line 1.
Use of uninitialized value $fn_y in string at -e line 1.
$ perl -wMstrict -le 'my $fn="x"; print "${fn}_y"'
x_y
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