Learn Finnish: Olemme laskeneet erät, paitsi että hävikistä johtuen meillä on puute. - We have counted the batches, except that due to the wastage we have a shortage.

Paitsi as a preposition (meaning "except") is used before a noun or pronoun, which it forces into the partitive case. But here, we are introducing a whole new clause with its own subject and verb (meillä on puute). When you want to say "except that [an entire clause happens]", you must use the conjunction paitsi että.

Why is hävikki (wastage) in the elative case (hävikistä) before johtuen?

Johtuen means "due to" or "resulting from." It is formed from the verb johtua (to stem from / to be caused by). Because the verb johtua always requires the elative case (-sta/-stä), the phrase built from it does too. So, "due to the wastage" becomes hävikistä johtuen.

Why is the object erät in the nominative plural instead of the partitive plural?

The counting action is complete and refers to all the specific batches in question, making it a total object. For plural words, the total object is identical to the nominative plural (ending in -t). If you were only counting some of the batches, or if the action was still ongoing, you would use the partitive plural: Olemme laskeneet eriä.

What is the difference between hävikki and puute here?