How are the donation percentages calculated for epics?

Both donation percentage and fleet member donation status are calculated at the same time. Donation contribution percentages are not individually calculated on their own, but rather donation percentages for each resource will differ. Energy > Planet Resources = Food > Coins

For example: (suppose the donation ratio of coins to food is 1:2)
Stage 1 >> 150,000 Coins
The donation percentage is calculated as follows
Member 1: Contributes 100,000 coins, 67%
Member 2: Contributes 50,000 coins, 33%
Member 3: Doesn't donate, 0%
Member 4: Doesn't donate, 0%

Stage 2 >> 15,000 Food Items
Total donation percentages are calculated as follows (including percentages from Stage 1)
Member 1: Contributes 7,500 food items, 64%
Member 2: Doesn't donate, 28%
Member 3: Contributes 5,500 food items, 6%
Member 4: Contributes 2,000 food items, 2%

The total sum of contributions is not 100% in my epic fleet. Is it a bug?

It's not a bug. It's designed that way to prevent any abuse of the epics.
If members have left the fleet by themselves or the members have been kicked out by the fleet captain, the contributions won't reset. To get the correct award from an epic, it is important to team up with people who can finish the epic to the end.

If you don't want people you don't know to join your fleet, you can turn on "Invite Only" in the fleet settings to only allow your friends to join your fleet.