After the death of her best friend, a teenage girl begins to notice and investigate strange inconsistencies in reality, attracting the attention of a dangerous organization.

You've provided a setup but not a goal for your character. Is it to survive? What will she have to do to accomplish this goal?

It's also not clear as to WHY the death of her friend has any connection to her investigating "inconsistencies in reality" (I also don't know what that means). Can you clarify that within the logline? (Did the friend die under mysterious circumstances?)

Can you find a better word than "girl" to describe your protagonist? Introvert? Prom-queen? Book-worm? Prankster?

"After the death of her best friend, a teenage girl must battle a dangerous organization that wants to wipe her memory when notices strange inconsistencies in reality."

...or...

"When the death of her best friend causes a teenage girl to notice strange inconsistencies in reality, she must battle a secret organization that seeks to wipe her memory."

Hope these help. They're more active than your initial version, and also give the protag a goal to achieve and reveal what she'll lose if she fails. By showing the protag's goal and the stakes in the logline, a reader will get a better sense of what your story is about and how it might play out on the page.

I like your concept. Think it might have legs. Best of luck ;-)