I think it could be easily attributed to the fact that most non-native speakers learn English at school by studying its grammar in written form, where the two words are distinct. Native speakers, instead, learn English as their spoken language, where the words sound basically identical to each other.
As a non-native, I learned "then" and "than" in different contexts, months if not years apart. I also learned them in speech and in writing at the same time.
Please don't quiz me on how to read bear, pear, tear, fear, spear, clear, and dear.