Started a fresh world in singleplayer. Spawned in some armor, syringes, wings, and an End portal. Took myself OUT of creative mode, went through the portal and flew up to the naturally spawned ender dragon with syringe in hand and left clicked multiple times. Syringe didn't fill up at all, but worked fine later when used on a wither instead. No ERRORS generated either time.

RFTools Version: 3.11
Minecraft Version: 1.7.10
FTB Infinity

It doesn't work on our server, with a vanilla Enderdragon.
Edit: Also, if you cheat/edit in a dragon syringe and try to build a dimlet out of it in the workbench, it will crash the game.

This is still an issue. I believe it's caused by the fact that everything you see of the dragon isn't actually an EntityDragon but is rather an EntityDragonPart (which extends Entity not EntityDragon)

Ah that's a good tip. I will check that out

Will be fixed in next version

Clarifying Question, are you using any mods which alter the end?

It is part of the FTB Infinity pack, so there are some such as Magic Bees and Draconic Evolution.

I'm pretty sure Draconic Evolution modifies the default Ender Dragon specifically so you can spawn new (harder) Ender Dragons with the resurrection ritual. I can verify that this issue happens on FTB Infinity 1.8.1 with RFTools 3.11 as well.