Plugin: Search and Replace

I used Search and Replace to update the URL that was originally https://www.mydomain.com/wordpress to just https://www.mydomain.com. However, it seems that some links have not been updated properly. The blog posts on my first page show up, but when I click on the button to go to page 2, I get an “internal server error” problem. Same goes for the monthly archive page from the calendar widget that should display all posts from that month. Can anyone help? Thanks!