Assuming this is an R4 compressor, does it have regular o-rings or the later sandwich type seals. I ran into this problem on my daughters car. basically the bolt would cross thread at an angle. I am talking about the bolt that is between the two hoses at the compressor.
I got a tap, carefully tapped the hole and held the line in place while I started the bolt correctly. I took the bracket loose that holds one of the lines in place on the back of the compressor above the manifold. This let me get the manifold in place and tight. Then I put the line bracket in place AFTER the manifold was tight. That was a few months ago and everything is still tight.