Can only send 1 character to "Collect Intel"

Homer has a task at the beginning of act 2, try tap the main globex building and use the task list there, you should be able to send the rest.

I did send Homer on the first Act 2 task (Sleeper agent right?)

The only character that shows up at the headquarters is Apu. I sent Moe and Cletus on some missions that were highlighted yellow with disks as the reward but even they don't show in the headquarters. Only in town hall.

would that be the dossier tasks?

No Marge and Krusty were for the next dossier tasks.

I've sent everyone that has an available event task but the headquarters remains empty except Apu.

You could try using the Town Hall to track down the missing characters you know have jobs to collect intel to see what task they are performing.
Are they on just their normal 4-hour tasks?

When they show in your town hall list, what did it say they were doing?

And when you tap the GO TO button, where does the game take you?

I have all my characters free and only send them on the 4 hour task of each event. None of them except the ones I mentioned had any event tasks available for them.

Today a few more characters became available again to collect intel so I don't know what's going on. I'm guessing by the end of Act 2 they will disappear again.

I'll use Marge as an example:
From the Agency Headquarters you should be able to task her if she is available.
http://a66.tinypic.com/2vv86xx.jpg
If not, got to the Town Hall Census, scroll to Marge and tap 'Go to'
http://a68.tinypic.com/1ghhqf.jpg
That takes you to Marge's task list where you should be able to select an event task.
http://a66.tinypic.com/29bhr3m.jpg

Ya within the headquarters there's only 1 character again but if I goto Marge for the example, her intel task is available but even when I send her (though it does reward me) she does not appear in the headquarters.

I don't even think I have the proper amount of characters with intel tasks. They're just simply not available to them. As if there is no event happening.

There's definitely some glitch going on.

The next simple step would be to do a hard close on your device. Restart and then check to see when you tap the HQ if the character tasks are there. If not, then uninstall/reinstall if your town is registered and you remember your login password, if not, contact EA tech support.