Thank you for contacting WPML support. I'd be happy to assist you further on this issue.
Please follow the steps to fix the issue:
1) Visit WPML>>Languages
2) Click on *Edit Languages* link of *Site Languages* section
3) Choose *Upload flag* option of language that you wanted to change the language.
4) Upload the desired flag image. You can use PNG file. Flag size should be 18px by 12px.
5) Save the settings and confirm the modification is working for you.