the map is created by Valve.

Whatever you can do in this map is (partially) intended by Valve.

If you do NOT want people to do certain things, download source SDK, go to hammer, make a block with CLIP and place it over these holes, then change the map to ctf_2fort_noholesonplacesthatannoyme instarespawn and all problems are solved!

Also, I dont see the problem,
This is just like building sentry when attacking dustbowl or shooting through the holes in cp_well.

I really don't see the problem, it's just like: "SOmebody builds sentries at the cp, thats not intended".

If you REALLY want to change this, report bug is the solution