Sounds identical to the problem I faced with my old Field & Trek water bag (a bit like what you get in big cartons of wine) and my current 5 litre plastic water carrier that folds flat. Both fine to fill in falling water, or running water provided it was deep enough, but hopeless in still water even deep pools.
I used to painstakingly fill them with my half-pint drinking mug but it took at least 30 scoops because when pouring the water into the carrier a proportion of it missed the narrow spout.
This has been overcome by buying a small folding funnel on eBay, so all the water goes in without losing any, while the process is also quicker with the 500ml plastic measuring beaker I now use, also from eBay. The latter is useful for measuring the correct amount of water to boil for freeze-dried meals, and it is lighter weight than the mug.
Prior to these I tried a 500ml drinks bottle cut to make a funnel but it soon got crushed and broken in my rucksack, while I found a whole 500ml bottle took too long to fill compared with a mug, and it was also extra bulk to fill my pack.