Common FRED Issues
From FreeSpace Wiki
Problem: I placed a ship in FRED, and now I can't deselect it by clicking in an empty area.
Solution: You probably have models and/or wireframes turned off, and can't see the actual size of the ship you placed. FRED still knows how big it is, though. Turn on wireframes or models, and if necessary zoom out, then try again.
Problem: When I play my mission, the background nebulae are showing up in front of the planets.
Solution: Backgrounds are rendered in the order they are placed. Make sure you don't place your planets until after placing all the nebulae.
Problem: None of the ships in my mission use their beams.
Solution: You need to either check 'All Ships Beam-Freed By Default' in the mission specs editor to free beams on all ships in the mission, or use the beam-free/beam-free-all SEXPs to free beams on a specific ship.
Problem: Some ships do not show up at all, even as wireframes. All I get is a green dot.
Solution: FRED hasn't found any textures for the ships. Add -jpgtga to your FRED shortcut to enable .jpg and .tga textures, as those are not used in retail FreeSpace. FreeSpace Open does, since the 3.6.10 build.
Problem: FRED doesn't seem to be using any of my MediaVP enhancements or other mods.
Solution: By default, no mods are enabled. If you launch FreeSpace with the mod of your choice, FRED will open with that mod loaded. To set FRED to always use a specific mod (for example, MediaVPs), create a shortcut to FRED2_open and add "-mod modname" (for example, "-mod mediavps_2014") to the command line. Note that, in the case of mods that depend on other mods (like, for example, ST:R, which depends on the fsport), you will have to enter the entire -mod argument as generated by the Launcher. For example, if you have a mod folder called yourmod, which holds all your data, and you want to use both that and the mediavps, the -mod commandline would have to be -mod yourmod,mediavps.