If you have only two spawns in your map (one for axis on one side of your map and one for allies on the other side) I don’t think it is necessary to fill it in: In the script they are only called when for example you have a spawnpoint owned by the axis team that get switched to the allies team, like for instance in fueldump or goldrush… So you don’t have to adjust your script…
Personally I think it just might be a glitch. So first I would delete all team_ctf_redspawn and create just one new one, give it a targetname: axis_spawn and a scriptname axis_spawn (you can call it whatever you want) , startactive and invulnerable flags ON and copy/ paste this entity so you end up with 12 team_ctf_redteam entities. Now do the same with the bluespawn but give it another script/targetname for example ‘allied_spawn’…
This is how I usually create my spawnpoints