It turned out that this extension duplicate some or all queries for each article you want to display. I don't understand why when JoomFish was trying their queries they were taking CPU and more time to respond so that was causing problems since articles were not totally displayed and the process in the server was just running like crazy and taking resources. They were blocking the database and also causing a big queue to process results in the database.
I found out when I ran a load test tool and found out all the queries with trouble. I decided to disable Joomfish but the problem didn't stop since the tool keeps duplicating the queries even though is not enabled. I had to uninstall and remove everything related to Joomfish and that helped, I have not had any other issue with performance.