I think you have admin level protection enabled and because they don't have confirmations, they can't use the commands. One thing to note is that the admin levels are not confirmed during the warmup period. This was made this way because otherwise there could be false alarms with incomplete authentications when the warm up ends and the map starts. Another thing is, if you look at them with the !list command, do they have any flags set. If I remember correctly, there is a 'C' flag set for the players who need confirmation. One more thing, if they have for some reason lost their stored confirmation keys in the clientside, then !setlevel is required to set both their level again and creating new confirmation keys. However, the admin chat will report these players if enabled.
The confirmation is done with !confirm command. Or alternatively, with !setlevel.