Generally, the common agriculture policy is a big thing in the European Union (Why does the Common Agricultural Policy exist?)
I read in many German articles that the lobby of the sector is extremely strong and many of the lobby members are in the conservative party (CDU) which was in power for a long time on the federal level and is in many states. I also expect that there is very strong lobbying within the EU going on.
Given that farmers in the EU have a strong lobby and are heavily subsidized why did the situation end up with strong farmer's protests all over the EU that resulted in abandoning environmental policies?
Maybe my best example is that you are not allowed to fertilizers (especially animal excrements) on your field in February. This is because they expect February to be a cold month and the field might be frozen leading to oversaturation of the minerals and hence a degenration of the water quality. However, the last February was extremely mild and rainy, thus the minerals would have been washed out (ok, they still end in the water, but I guess more dilluted) and thus the problem would not occur, making the law useless for this particular February. (Sorry if this is a poor example, I am happy about edits with a better one or corrections!)
So the main conflict is regulating a sector which has a huge overproduction while being harmful for the enviroment. One could expect this to be done better given the lobby strength.
Clarification/Edit given the comments: Given the strength of the lobby, how could things get so much out of hand that there are so massive protests? And given the need for rules and the fact that they were passed, why did the lobbies not help to make them workable or block them right away? In an ideal world making workable rules would be exactly what lobbies are for.