Big hint on the problem (possibly)! I just realized that issue is with inventory items in which you don't have stock in. I purchased a pound of Acidulated malt, updated my inventory and went to the brew link. This time it grabbed Acidulated malt (now in stock) vs trying to switch it to Aromatic. While the Rye and Wheat are physically in stock, I don't have them entered as such so the system is trying to swap them out with Pale and ESB.
Went back in added a value into the Rye inventory, Brew again and it grabbed the correct item.
Hope this helps fix the problem.
Ah that does make more since then.
Some time ago, the inventory deduction logic was changed. I think it was this update -
https://www.brewersfriend.com/forum/threads/july-updates.14925/#post-143380
The general step in logic is that a match is search for in this order, always looking for the closest match that has an active positive inventory qty.
1) Exact name match, exact property match.
2) Similar name match, exact property match (looking at grain type, color, ppg, diastic power, and brand).
3) Similar name match, similar properties.
Since you brewed a recipe, but had no acidulated malt in stock, there was no match found from your active inventory, so the deduction looked for the next closest match and found aromatic being the most similar. When you deduct, it should show this, and allow you to either cancel the inventory deduction, or choose from a dropdown menu of what else you have available.