As per mdoc(7), \&. is needed to escape a literal period. That said, shouldn't .Pa be used here rather than .Sq?
Index: portbump.1 =================================================================== RCS file: /cvs/ports/infrastructure/man/man1/portbump.1,v retrieving revision 1.4 diff -u -p -u -r1.4 portbump.1 --- portbump.1 25 Jan 2016 17:27:24 -0000 1.4 +++ portbump.1 29 Apr 2016 04:19:11 -0000 @@ -59,7 +59,7 @@ information will be ignored. doesn't care about actual subdirectory portion of .Ar portref , so you can freely pass -.Sq . , +.Sq \&. , .Sq ../foo or anything else like this. .Pp