Latest version of KSPCommunityFixes reports on some potential memory leaks on scene changes. A quick look in the log after scene change to Flight Scene shows 1 potential location in ShipManifest where a leak might exist:
[LOG 20:42:39.428] [KSPCF:MemoryLeaks] A destroyed ShipManifest:SMAddon instance is owning a onGUIApplicationLauncherDestroyed GameEvents callback. No action has been taken, but unless this mod is relying on this pattern, this is likely a memory leak.

This has been addressed in the upcoming 6.0.7.0 version. currently in the dev branch.