Not sure whether it is due to the new battery firmware update, found that all 3 of my batteries for phantom 4 are hot when I took them out from storage and I could not charge them due to the heat.

This is the first time I am encountering this after 2 months of usage.

Anyone facing the same issue?

Have you updated each of the batteries ? If not then they will need updating. Also check battery settings in DJI GO App (with device connected to controller and aircraft powered up). The advanced setting shows a time to discharge in days ( can be set 1-10 days, default is 10), if the batteries have been inactive then they will start discharging themselves after this time. They will discharge over a couple of days (I believe, but I've not checked) to a storage level of 50-65%.

I haven't noticed this..   Are you just going by feel, or are you reading the actual battery temperature in the DJI Go app?  What are some of your readings after a flight?