I've noticed two bugs while playing a couple games that involve the bonus (100%,300%,700% tiles).
First...if you build a Farm on a bonus tile, then decommission it, the population increase caused by the bonus tile remains, and there is no way to remove it.
This is only really a problem if you want to lower the population to fix morale. In any other situation it's actually helpful.
Second...On a 700% bonus to manufacturing tile, my manufacturing ability went DOWN when I upgraded a manufacturing center to an industrial sector.
Can anyone else confirm these?