The time you get now to drop one in with it being stolen from you has been shortened quite a bit from where it used to be. What that exact number is I’m not sure but do know it’s somewhere between 30sec and a minute.
Extras can only be dropped into Gyms that are being battled if there was spots available before a battle has commenced.
If a Gym had a full 6 ijn it and you start to battle it and and knock any out, no more can be added to that Gym by the opposing colour.
If the Gym only had 4 in it, 2 more can be added at any stage through the battles while your knocking them out.
In your case after the first one was added up to 5 others could be added at any stage while they still had at least one still in the Gym. They would not have been able to just keep adding others in excess of the total combined of 6 so you should have just kept going and knocking them out.
Advice to all, is know what your going to put in a Gym before you decide to knock one down so it can be done quickly.