Vinegar is from Acetobacter, a common spoilage bacteria. It converts the alcohol in your cider into acetic acid (vinegar).
What cleaner/sanitizer are you using? You need to make sure that everything that touches your beer...spoon, siphon, hydrometer, tubing, spigot on bottling bucket, etc...is cleaned AND sanitized. <- Those are two separate processes.
Unfortunately, this bacteria is everywhere, so you have to be very vigilant about your sanitation.