The most likely cause of this is that all of the gym's slots are full, which means you will not be able to add another Pokémon until the gym is upgraded. Gyms can hold a number of Pokémon equal to the gym's level, so the gym in question is likely only level one, and its slot is already full. To increase a gym's level, you must win friendly "battles" (training) against the gym using only one Pokémon (as opposed to the usual six). Every time you beat a Pokémon at that gym, its prestige will raise, eventually leveling it up and adding another slot. At this point, you should be able to add a new Pokémon to the gym.
As Riley mentioned, the button will appear in the bottom left corner of the gym when there is an empty slot, and any Pokémon that you wish to place in that gym must be full health.
Can more than two players simultaneously battle a gym?
Yes, but not in the double battle style seen in the Gameboy/DS games. Both are battling in separate battles to reduce the prestige of the gym and thus take it down.
As @Teaganator describes in his/her comment below: "You can be in the same battle instance with a teammate battling a gym. How that works it both players take damage as if they were alone, but they both deal damage at the same time."
You can also tell if you are battling with someone else because an icon will appear on the left side of the screen under your Pokemon's health that will tell you the nu
Can gym members of X and Y fight together against gym Z?
I would assume so, only because of the way I understand battling a gym as explained above. Both are trying to reduce the prestige of the gym.
Do players teaming up together have to start the battle within a window of
time or simply as long as a battle is in session?
No need to start at the same time because you aren't battling together as a unit. Just attacking the gym simultaneously.
I don't know for sure, but from what I witnesses last night, as long as the second(or subsequent) person joins while the first(or previous) is battling, they will be grouped into the same battle. Now I'm not sure if starting at the same time will cause a problem and create 2 "instances" of the battle. I would hope/assume not though.
Can you team battle at your own gym with players of the same color?
I'm going to assume instead of battle you mean train. In which case yes, multiple members of the same team can train on a allied gym at the same time.
This I do not know. I didn't test this last night. I encourage those in the comments to chime in and I can edit this part.
In the event that you and an ally remove the prestige from an opposing
faction's gym, what dictates who places a pokemon there?
Whoever gets their Pokemon in first. If you're playing with a friend or someone on your team you might want to coordinate what you're putting in. If you think you and a mutual enemy took down the gym then you want to get a Pokemon in there ASAP to claim it.
Edit Note: Last night after defeating an enemy gym, 3 players put in 3 Pokemon immediately after taking down the gym. I wasn't aware you could do this. I thought you had to put in one, increase prestige, put in another, etc. Was this a glitch? And if not could someone explain this to me?
In Conclusion:
There is no special condition when battling as a team. You are concentrating your efforts with another player to reduce the prestige of an enemy gym or raise the prestige of an allied gym faster.
Also I was REALLY wrong initially.
Also, thanks to users Theyna and Teaganator in the comments for being right when I was wrong.
Best Answer
The gym you're "attacking" is controlled by your team - you're training it.
When powering up friendly gyms, you are limited to one pokemon.
Update: As of 0.41.x, powering up friendly gyms are now 6v6.