Issue with specific repo - unable to read/write files in EC2 instance

Did anyone faced below issue?

Please help with this strange problem that i am facing with aws EC2 instance (ubuntu). I have launched a EC2 instance & installed git to clone my repo. all good until this, but i am unable to read/write those files though they exists in the same path. observed the same behavior in Amazon Linux instance as well.

ubuntu@ip-172-31-54-19:~/win2win$
ubuntu@ip-172-31-54-19:~/win2win$ cd $HOME
ubuntu@ip-172-31-54-19:~$
ubuntu@ip-172-31-54-19:~$
ubuntu@ip-172-31-54-19:~$ cd win2win/
ubuntu@ip-172-31-54-19:~/win2win$
ubuntu@ip-172-31-54-19:~/win2win$ cat myscript.sh
cat: myscript.sh: No such file or directory
ubuntu@ip-172-31-54-19:~/win2win$
ubuntu@ip-172-31-54-19:~/win2win$ ls -lrt
total 28
drwxrwxr-x 2 ubuntu ubuntu 4096 Apr  5 09:21 templates
-rw-rw-r-- 1 ubuntu ubuntu  792 Apr  5 09:21 sampleIDs
-rw-rw-r-- 1 ubuntu ubuntu 2614 Apr  5 09:30 myscript.sh
ubuntu@ip-172-31-54-19:~/win2win$
ubuntu@ip-172-31-54-19:~/win2win$ pwd
/home/ubuntu/win2win
ubuntu@ip-172-31-54-19:~/win2win$

TIP: i have started pulling/pushing changes via GitHub Desktop in windows and also in another macbook with this repo, thats the only different i have observed.

I have tested a different repo in EC2 instance and its working fine, the working repo is not used in GitHub desktop recently so i am suspecting on GitHub desktop.