The catapult lists a crew that isn't just an orc warrior along a modified Troll, yet the rules for troll upgrade are quite clear that it should just be a Troll from that army list.

Are they supposed to be different from normal orcs and with that odd troll?

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I am a bit confused by the structure of your questions but I believe that you are asking if the siege engine crew and troll are different in any way from the regular profiles.

The crew do have their own profiles and keywords so they seem to be different from regular orcs but only as far as it relates to interacting with the siege engine and buying gear. The trolls are also exactly the same as the normal trolls except for their interaction with the siege weapon and the buying of gear. So, they are both different but not in a very meaningful way. I hope I got the gist of the question but if not, I'll try again.

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"Draw your sword with a heavy heart, but swing it with a heavy hand"

Page 123 of the armies of LotR, check the profiles listed in the Mordor War Catapult.

All the other siege engines seem to list the crew just for convenience, it's a copy of the normal profile.
This one however has different profiles listed (orc warriors have C 2, C 3 on this page, Mordor Trolls have C4, C3 on this page)
I'm assuming it was a mistake

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Oh your right. I would say it was a type-o but I cannot see any reason for it to exist if the regular profile would have been intended. I'd argue for ignoring it and using the rule books crew formula instead. Keep things simple.

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"Draw your sword with a heavy heart, but swing it with a heavy hand"

Can the troll move away from the catapult if he desires so? Or is he stuck 6 inches from the catapult? What about crew?

Lets say, an enemy is overraiding the catapult, cant the crew escape? Or if they simple want to join a melee fight elsewhere?

There is a line, on the first page of the siege engine rules I think, that says the crew can't move more than 6in from the siege engine unless it is destroyed. The troll is counted as a member of the crew according to the entry for the troll upgrade. As such, the troll is subject to that restriction. You are, of course, free to move the engine about to get the troll into combat if you so choose.

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"Draw your sword with a heavy heart, but swing it with a heavy hand"