I vote for clean and sanitize the equipment. I use my bottling equipment for sour and non-sour beer and do not have crossover infections.
Ok, then advise as to your cleaning and sanitizing routine - prolonged PBW soak?
Really nothing unusual, except maybe a longer soak.
As soon as I finish bottling whatever I'm bottling I immediately get in and start cleaning. It's far easier to get everything clean while it's still wet. There's no time for brett to cough up a biofilm and hide itself. Hot water rinse and if there is visible debris on/in the equipment then I scrub with a soft sponge or for my one gallon glass jugs I use a bottle brush. Soap is used if there's a lot of debris. Then rinse several times, fill with hot water and mix in oxyclean. I let it soak for a week and then dump, rinse several times and let dry. Then I sanitize with starsan before the next use.
Some comments above discussed possible infections in the bottles. That is certainly likely although I would compare infected bottles side by side and see how similar the infection is in taste and aroma. I would be surprised if an entire collection of 40 or whatever number of bottles had the exact same wild yeast or bacteria.