Urls with index.php?

Hello SI Team

I am a self confessed URL idiot.

Here is the menu structure for my site:

HOME (SP Builder Pro)
https://finalbug.net

PLANS (Pay Plans)
https://finalbug.net/index.php/store

GROUPS (Easy Social)
https://finalbug.net/index.php/groups-learn-post-production-socially-fcpx-and-more

NETWORK (Easy Social)
https://finalbug.net/index.php/network-final-cut-pro-post-production-professionals

BLOG (Easy Blog)
https://finalbug.net/index.php/blog-final-cut-training-resolve-etc

VIDEOS (EASY SOCIAL)
https://finalbug.net/index.php/videos-learn-fcpx-davinci-workflow

STREAM (EASY SOCIAL)

https://finalbug.net/index.php/stream-social-learning

From GROUPS through to STREAM

“index.php” appears in the URL!

Is this normal because I have a feeling this was not the case in the past?

Maybe there was a feature added recently that changed how URLs behave?

Is there a setting some where to remove the “index.php”?

Surely it is not good for SEO etc?

thanks

Paul