There were a lot of clues that something was up. I think we have to assume, given everything that happened in previous books, and if we can leap forward a bit, at the end of OotP, Dumbledore is aware of a lot of things going on at the school for which he has no reason to know. In OotP he speaks of being fully aware of Harry's adventures, in CoS he is aware Harry is and the others are under the invisibility cloak in Hagrid's hut, despite there being nothing to hint at him being told or seeing clues. He just knew.
If we carry that through, the idea that things go on in the wizarding world and he knows about it, even if we can't explain how, we then need to look at what we (and dumbledore) know:
-Voldemort is working on coming back
-Someone hoodwinked the goblet with serious dark magic.
-Someone at Hogwarts stole ingredients for polyjuice potion this year (dumbledore would be aware the stolen ingredients this year were not the same as two years previous)
-Dumbledore is (probably) aware of the news of Crouch Jr's supposed death in azkaban, and also aware of the limitations of Dementors' sight
-Crouch Sr's previous devotion to ending Voldemort and his followers, would make him an unlikely candidate to be working for Voldemort, but he was clearly somehow linked to it (winky at the cup, winky with the dark mark, crouch sr looking where winky had been when stunned, crouch sr's behaviour in general (working via letters etc), crouch sr's behaviour when harry met him as he was breaking free of the imperius curse)
-Dumbledore was clearly looking at the Crouches (when Harry discovers the pensieve he is looking at Crouch and Crouch jr related memories - the other followers in those memories were all accounted for)
-With so many guests at the school, a trusting nature, and a convincing performance by Crouch jr as Moody, suggests the above led to Dumbledore suspecting Crouch jr, but not being able to identify who he was masquerading as until the moment he took him away from the maze.
"You'll find it's a very small universe when I'm angry with you"
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