You can't do that!
If only I had a pound for every time someone has said "you can't do that" to me, I would be a very rich woman today!
It's common that when staff think they can get away with things, they may be a little bit upset when you start to lay down the law. This is even more common when you have policies and processes in place that just aren't being following by some department managers.
So how can you change that? Easily!
First of all, send the offending managers on refresher training to remind them of HR policies, why the exist and how to apply them. Then, simply remind all staff that there are policies in place that need to be applied consistently throughout the company. You can re-issue key policies or post a summary of them on the notice board with reference on where to access the full policy. Give it a couple of weeks to make sure that everyone has had enough time to review the policies ask any questions. Then start following the processes.
For example, if you want to crack down on multiple short-term absences, follow the process above then start having return to work meetings and stage 1 absence meetings with staff as required. When you tell them that you will be making a record of the meeting that will be kept on file and any further absences may lead to disciplinary action, you may well hear them say "you can't do that". This is when you politely remind them that you can in fact to that and you will if need be. Refer them to the policy for review and offer to answer any queries regarding the policy that they may have.
Remember, you have the right to manage your staff and it is important that all department managers follow the same processes and apply them consistently.