We have received reports that Trainers haven't been able to collect their Defender bonus after the Gym update. We’ve investigated many of these reports and have not been able to reproduce any bugs related to this issue.
Trainers no longer earn the Defender bonus for each Pokémon they have in a Gym each day. Instead, Pokémon earn PokéCoins by remaining in the Gym for as long as they can. The longer the Pokémon remains in the Gym, the more PokéCoins you’ll earn (up to the maximum bonus for the day). You redeem your PokéCoins only after your Pokémon returns from the Gym.
You can redeem a maximum bonus of 50 PokéCoins per day. Once you've reached the daily limit of 50 PokéCoins, you won't earn any more PokéCoins until the next day. If you have more than one Pokémon return from Gyms in a single day, the maximum bonus for the day is still limited to 50 PokéCoins. If a Pokémon returns after multiple days in a Gym, the maximum bonus for the day is still limited to 50 PokéCoins.
The maximum daily bonus changed with the recent Gym and Battle updates. Please note that the maximum bonus limit is subject to change and may vary from time to time.
On Tuesday, July 18 PDT, there was a short period of time in which Defender bonuses were not being awarded. This issue has since been resolved.