I know what you're talking about since I have experienced it before, but I have not encountered the problem often in the past year or so. Perhaps you were just using it during a dry spell from the NewPipe developers or F-Droid. A number of useful features have been added during the past year, such as the ability to view live streams. A few quirks also exist, such as feeds displaying videos that are posted in the future.
As for the recommendation engine, I prefer gaming it. NewPipe is wonderful because it does not feed it. I have a special profiles setup on my desktop for when I want to feed it. This approach works wonderfully for discovering new channels, allows for multiple profiles to get recommendations for different viewing interests, avoids polluting recommendations based upon a single odd-ball view, and allows finer grained control over the information that I feed Google.