I completely removed the vault and imported from Lastpass this time. It's still same. I used CSV format for LastPass.
If I click the extension button directly, it doesn't show any matched item, but if I use command + / shortcut, it shows them correctly. After that point the issue is fixed for the website completely. But I have to do this for all websites. I think something is wrong with Enpass to check matched domains by clicking the extension icon.
Although this fix the problem for some websites, I realised that it mixes up matched items for that "fixed" websites. Now, it shows both matched websites for the current website and other ones for another websites together. I checked the domain fields, but they are completely different. If I run the same shortcut (Command + /) it shows the matched items correctly, again. As I said, it's mixed up as I fix the problem on more websites.