This is because the swords skill (in MCMMO) is used for PvP. If you were able to get to level 10k+ by killing mobs from spawners, that'd be really op. This is intentional, not a mistake.
You can however grind swords levels from natural, unstacked mobs that spawn on your island (or other islands. Try /warp platform for a dark place that mobs can naturally spawn.)
(ps., you can still get swords levels from spawners if it's an unstacked mob. ie., it's just 1)