I have a tube of CLU that is around 5 years old that I use for delids. I re-lid with black silicone, so I don't even have an opportunity to check how well the IHS and die mated with the CLU.
I haven't had a single problem with the old CLU, though. Performance on all my delid/relids has been excellent.
It's possible by removing the lid, the surface tension of the liquid metal pulled it away from the center and makes it look like it was dry in the middle. If you didn't have any measurable thermal issues, I don't see any reason why you should worry about it.
Less is definitely more when it comes to liquid metal TIM. You don't want to put enough that it squishes out the edges around the die.