I couldn't reproduce this, but confirmed this is
not a bug and is working as intended. I've updated the wiki to be a bit more clear.
The 3-layer limit (for an enchanter without Seal Magic) is only three layers:
- Per enchant category
- Per item
- Per enchanter
This means you may put up to three of one enchantment category on an item, and are free to add more layers of other categories e.g. a 3 Death/3 Accuracy Pistol. It is also possible for multiple enchanters to work together to lay enchants up to the maximum, e.g. if you got a 3-Death Pistol from someone else, without the Seal Magic skill you're still free to add 3 Death layers of your own for a total 6 Death Pistol. You only pay the MP cost for
your own cumulative layers when you do this, so there's some incentive for collaboration.
While I don't know all the circumstances (as this is an old thread) probably the three layers on the item in the bug report were made by another enchanter, so you were still free to add more layers of your own.