Several of them are separate series - SF&O, 80 Page Giant. List them under a See Also at the bottom if you have to. JLA: Earth 2 is just a separate thing with "JLA" in it. New Years Evil: Prometheus doesn't even have that... Trim the list.
Again, template works. You just don't fully understand how it works.
I don't want to claim any of these opinions are policy just yet, but here's what I think:
Crossover books starring the JLA and a non-mainstream continuity team (i.e. wildcats, witchblade, ninjaturtles, predator, cyberforce) are not Specials belonging to that volume. They're just one-shots that star a version of the JLA, which may or may not be that of the volume in question.
One-Shots that don't specifically reference the continuity of the volume in question - i.e. A League of One are not necessarily "Specials" to the volume, but rather just books that star the justice league. A League of One, for example, is technically a graphic novel. It came in hardcover, and it had nothing to do with anything going on in JLA Vol 1 except that its characters starred in it.
Continuity specific stories like Prometheus or Our Worlds At War are definitely specials, belonging to the volume, which belong on the volume page.
Open for debate, but Tupka's response is basically mine, there.
There's no point in getting bogged down on whether something is a "bug" or a "capacity limitation": bug report software regularly includes feature requests and things that aren't strictly "bugs". The problem was still what I mentioned before which is that the template couldn't accommodate all of the entries.
Since there is no documentation about whether or not a Secret Files is a "special" and they are routinely included as specials (e.g. Titans (Volume 1)), it's hard to know what to do with them but I've already edited the volume page to be able to display all of the relevant issues. Everything released as "JLA: [foo]" from 1997 until 2006 is now on that page.