[iceeedr]

Never faced such problem, what version of amx are you using? Anyway, here are some corrections to your code.

public SwapTeams()
{
    new players[32];
    new playercount;
    get_players(players, playercount, "h"); // 'h' to not include hltv
    
    new i, id // do not create vars inside a loop
    for (i=0; i<playercount; i++)
    {
        id = players[i]

        if (cs_get_user_team(id) != CS_TEAM_SPECTATOR && cs_get_user_team(id) != CS_TEAM_UNASSIGNED) // You also check if he hasn't chosen any team yet, ie "unassigned".
        {
            cs_set_user_team(id, (cs_get_user_team(id) == CS_TEAM_T) ? CS_TEAM_CT : CS_TEAM_T)
        }
    }
}