Does this issue still persist on your system?
If yes, please have a look at the following article:
You have mentioned that you have installed the latest version (2.5) for D3 Tree and D3 Network Extensions. Therefore, you should be fine with D3 conflict.
You have mentioned you are using version 2.0.4 of Custom Chart Widgets Extension, and that version uses some special characters that require the JAVA encoding UTF-8 to be enabled for Tomcat (as recommended in our ThingWorx Installation Guide). Could you please confirm if you have UTF-8 encoding? If not, could you please enable it and see if that fixes your issue?
Additionally, as Polina mentioned, if the issue happens on some browsers only, you could also try to clear the local cache of the affected web browser and see if that fixes the issue.
I hope this helps!