Troubleshooting pex leakage
It would be ideal to know what kind of connections you have on the manifold. Often the connectors can be replaced but it kind of sounds like you don't have that option (or why would you ask?). 

So, if you have barb connections, then yes, you have to be careful cleaning them... scratches cause problems. But if there is enough length on the barbed connector for two clamps or rings, that might work. You would want to put the rings adjacent to each other on the pex, and use the crimp tool to crimp them at different angles. Or use a different crimps or clamps like ULTRA-LITE COMPOSITE HANDLE CRIMP TOOL FOR STAINLESS STEEL PEX SLEEVES or Apollo PEX Cinch Clamps.

I suppose that if you had flare nut style fittings, it would be obvious that you could replace the parts, so there's no sense in my mentioning it any further.

Alternatively, if you have a shark-bite style connection, the tube support liner is what usually needs to be replaced. You should be able to remove the support line insert and replace it (depending on the manufacturer). Here's a link for pdf instructions from Shark Bite: http://www.sharkbite.com/sharkbite/wp-content/uploads/SB_Inslltn_Instrctns_2014.pdf

Here's a screen shot image of a google search for generic tube support liners for shark bite style connectors: