No they can’t. Money owed (or in dispute as owing) in relation to specific items, e.g. repairs to common property for damage down by an owner, do not form part of the levies. So if an owner is invoiced for something like that, and they don’t pay it, the OC can seek to enforce it by normal channels but it doesn’t come under the category of levies. For example, if that amount went unpaid but the levies had been paid, then the owner would be financial.
You seem to be saying that you have disputed whether or not you are liable for this amount. In that case the managing agent did not have the right to apply your levy payment to that invoice. They don’t need to consult with the EC, they should just reverse it in their books, which is easily done.
Also any interest accrued in respect of the unpaid levies should be reversed.