The rem command supports one argument, namely /?, and it is greedy for it. Your URL contains that string.
The = is a standard token separator (just like SPACE, TAB, ,, ;), and so the remainder seems to be interpreted as another (invalid) command.
Putting the remark text in between quotation marks helps here since /? is no longer detected:
rem "https://sourceforge.net/p/jedit/bugs/4084/?limit=25"
When you write this:
rem/ https://sourceforge.net/p/jedit/bugs/4084/?limit=25
the /? portion is no longer detected too. However, special characters like &, <, >, |, ( and ) are then recognised.
Another alternative is to use a ::-style comment, which is actually an invalid label (labels begin with a :, see goto /? and call /?):
:: https://sourceforge.net/p/jedit/bugs/4084/?limit=25
Special characters are not a problem here, but this must not be used within a parenthesised block of code.