Occasionally, LingQ is buggy and doesn’t add a word you’ve already seen to your LingQ list. I have the settings so it automatically adds all blue words to known when I go to the next page, and occasionally when I go back to re-read a text there will be one blue word in the middle of the page that LingQ somehow missed. But this will be one word out of very, very many.
It’s fine to add slight variations of a word to your known word lists. The way LingQ is set up with its Beginner 1, Beginner 2, etc levels is it is expecting you to have high word counts due to including words like that. Otherwise you would need far less than around 9,000 words to get to Intermediate 1.