Well, there is 60 minutes cooldown for your bonuses to take, else they will change. If you will not take your bonus in time - it will dissapear after your 60 minutes will be deplited. Also, someone can attack you to steal your bonus, in this case it will change. Probably there was a guy who was waiting for last seconds to steal your 100 gems so you will have no time to revenge and get it back, so your bonus have been changed to chest.

Also there is chance to get good things from chest:
i am lvl 40, for me its like 20% chance to get lvl 1 or 2 Gem from chest. Also about 3-5% chance to get one Star. Rumor says, you can also find sanctify cards to improve your heroes stats.