Code:
alias -l add.pts {
  if %point.off return {
    writeini -n Points.ini $1 Points $calc($readini(Points.ini,$1,Points) + 1)
  }
}

on $*:text:/!points (add|remove)/Si:#:{
  if ($nick == YOURNICKHERE) {
    if ($0 < 3) { msg # Insufficient parameters: Use !points <add|remove> <user> [number] | return }
    writeini -n Points.ini $+(#,.,$3) Points $calc($readini(Points.ini,$+(#,.,$3),Points) $iif($2 == add,+,-) $iif($4 isnum,$4,1))
    { msg $chan $3 now has $readini(Points.ini,$+(#,.,$3),Points) total points. }
  }
  else { msg $chan This command is only available to the owner of this channel. }
}


I don't know where you're all picking up code like this, but please stop spreading it around. The first alias is nonsense, and you don't surround arbitrary lines with braces. Aside from syntax, it's good to give meaningful names to variables instead of using $3, $4, $5 directly throughout your code.

Code:
alias -l add.pts {
  if (%point.off) return
  writeini -n Points.ini $1 Points $calc($readini(Points.ini,$1,Points) + 1)
}

on $*:text:/!points (add|remove)/Si:#:{
  if ($nick == YOURNICKHERE) {
    if ($0 < 3) { msg # Insufficient parameters: Use !points <add|remove> <user> [number] | return }
    writeini -n Points.ini $+(#,.,$3) Points $calc($readini(Points.ini,$+(#,.,$3),Points) $iif($2 == add,+,-) $iif($4 isnum,$4,1))
    msg $chan $3 now has $readini(Points.ini,n,$+(#,.,$3),Points) total points.
  }
  else { msg $chan This command is only available to the owner of this channel. }
}


And if the channel owner's name matches the channel you can avoid hard coding it as so:
Code:
if ($mid(#,2-) != $nick) return