it usually means there are various items using the same id number.
check all units, alliances, diplomatic relations etc, that you have changed and/or added and make sure they do not have an identical type AND id with another item.
It is also possible that you have two countries owning the same province, check that each country you have altered is the only one owning a certain province. Also check that you don't have a duplicate entry in the same file (for example CSA having two entries for owning Texas, or two entries of Texas being a national province and so on).
The best way of modding is the agonisingly slow method. Make a set of changes and then test them in game, before moving on to more changes, that way you can quickly isolate what may be causing errors.
Good hunting, and good luck.
Ayeshteni