I dont get any special problems any longer with enemies - that was a long time ago.
In all honesty I have still after all the time I have been working with FPSC not gotten around to testing out enemies and their AI etensively so I really cant advise any users a great deal on problems they may face.
The only enemies I have currently functioning work well for their situation in gameplay. I do know in the first instance some of the AI script files dont work well with the enemies as they behave as if they cant see the player and for some strange reason one of the first animations the AI script files call when they detect the player is - reload - by which time they have done so they are usually dead - killed by the player.
Personally I currently use the Cautious and Strafe AI scripts on some enemies in combination which seem to work fairly well and also one of the "Hang about and then attack the player combinations" which move the enemies towards the player on sight and when within range calls the shoot/straffe animations if the player moves away the AI calls the follow command and the enemy follows the player endlessly until he calls the attack routine again when withing range. This also works well and is a good combination, although I have edited the default scripts a little to improve them
If you open up the various AI scripts and look see the description of what they do then you should be able to use one suitable one in Main and one in the Shoot properties of the enemy. Using two differeing behaviours - mixing and matching until you find a good combo you should get a result even with the default scripts.
Some things to remember are that you can affect the way enemies behaviour considerably with a little simple adjustment to their properties in editor by changing field of view and so on. Dont be afraid to experiment with the settings - if it worries you make a copy of the settings by writing them down on paper or take a screen grab as I do, then if things go wrong - put the settings back as they were.
You can aslo quite easily improve their behaviour in script by simple changes to their attack ranges and so forth. If you cahnge any scripts make sure you back them up first so you can easily to back to the defaults if need be.
One more important thing - most enemy entities will have physics applied by default - if these are necessary and some times they are as in certain circumstances for unknown reasons with physics off entities dissapear from the level - the same entity placed at another location or level height will behave in the reverse manner - FPSC strangeness again Im afraid. The point being if physics have to be on set the weight and friction to 500 for each or the emnemies wont be able to move around properly or even at all. Which is why some users cant get them to move. If poosible turn enemies physics off completely as as a general rule they are not needed.
Waypoints wont or should not affect the enemies behaviours - the reasons for poor behaviour lie largely elsewhere. Dont attach enemies to paths unless absolutely necessary for your game design which in many case it may well might be.
Eventually users who get to be experienced with FPSC will be able to control enemies movement along waypoints and their behaviours at the various point locations or in relation to player proximity and so on. Its a fairly arduous and frustrating task and has to be set up individually for each individual gameplay scenario where the player encounters an enemy but the result in apparent enemies quality of AI can make it a worthwhile excerscise as it gives some futher means of control to what the enemy does and when it does it. Left to their own devices they become a little confused sometimes and appear to be a little thick to say the least, paticularly when it comes to obstacle avoidance which is relatively non existant in FPSC enemies.
A note on waypoints - unfortunately they and other FPSC entities such as trigger zones can become more than a bit of a pain - as placing a number of them one above the other at different FPSC level height locations enemies or other entities get confused as to which level the path they should follow is on and with numerous enemies on paths it could get to be a mess. As said this also happens with other entities in regard to the player too so if you place a trigger zone or player checkpoint in a room in one level and go upstairs the player can trigger the zone or player checkpoint from the room above. Quite a serious problem really which could do with some attention from TGC. Editing or writing special scripts for some things may overcome this by reducing distances on trigger proximities.
Most other silly behaviours are down to bugs or errors in the script files linked to enemy animations or other unknown reasons. Usually if you keep trying you can overcome some of the silly ones. Effort will be rewarded - except for anything thats well known as an issue with them most erronous behaviours are down to users needing to make some adjustments. The real bugs if any that exist with enemies the user can have no control over.