@Ajay Sharma
Without knowing what system you’re using and any of the details of the project:
1- have the roofing contractor do an inspection of the roof. You’d be surprised how simple the issue can be sometimes. It may have even been an MEP contractor that punctured the roof after the roofing had already been installed.
2- Most roofing manufacturers will require that a flood test be done as part of their warranty. A hose test is more appropriate for facades; not roofs (unless testing parapets). Some states like Florida even mandate flood tests in their Building Code. You can do an isolated flood test if you think you know where the leak is coming from. Contact the roofing manufacturer and they’ll walk you through the process.
3- I didn’t see any photos but ponding is common and not that big of an issue. Concrete guys never get it perfect. If the designers didn’t go with a conservative pitch, then there’s bound to be small areas where you get ponding. This doesn’t translate to leaks so long as your seams are sealed properly.
4- For the next project, hire a building envelope consultant like myself ;P
Good luck