Please do not post bug report if "all bonuses don't work" (and sometimes, even if "one bonus doesn't work").

Bonuses are not Effects

You probably need to ckeck in the rules the difference between "Effect" (which is always triggered when you pay to place a card) and "Bonus" (which is triggered only if you pay with and only with matching cards).

Bonus and effect are NEVER triggered if you place a card freely thanks to the effect (or the bonus) of an other card.

Shrubs are not Trees

Another one of the main reasons for "fake bug report" is a confusion between SHRUB and TREE. All cards that refer to "tree" doesn't work with "shrub" (ants, mushrooms, fat dormouse...)