Who issues the transcripts that applicants are asked to upload for a PhD application?
The basic problem is that different countries (and potentially different universities within a country) have different standards about what constitutes a program of study and what official documents they provide.

I did my studies in two different Australian universities - both provided a certificate at completion and a transcript. The transcript is essentially a list of all the subjects I studied and the marks. In Australia (at least for the programs I did), there is no overall grade on the certificate. That is, the certificate just says that I completed the course but doesn't say 'cum laude' or 'with distinction' or anything else that US universities might expect. The transcipt is used instead to provide information about the student's skills. One of the universities also supplied a third document, which provides a description of the program of study (eg number of years, what a major is) to help international universities understand what the qualification means.

I don't tend to need these when applying for anything within Australia because the universities have systems in place to communicate with each other. However, they are always required whenever I am applying for anything at any university outside of Australia.

Your university should be able to provide you with something official. The best area to ask is probably whichever administration group is responsible for providing the certificates when you complete. If you don't have anything official, you could provide your results notices and the contact details of whoever at the university is able to confirm they are correct.