Project requirements can be very different between various projects. Sometimes like this you have designers who are very precise, and that doesn't necessarily mean its a problem.
Where it becomes a problem is with the current framework and how the requested adjustments affect the overall project scope and timeline. Make sure that you inform the Project Manager that the framework you are using doesn't make it easy to make these adjustments and that they will need to budget more time for these tasks.
All you need to do is pass on the information that the Task XX3 is going to take longer than the estimated 2 hours; and explain why.
Its not your place to debate the purpose or use of these features... that is what the Project Manager is there for. Let the PM take it to the designers and owners of the project. But it may also be just as out of his control as it is yours, and at the end of the day you are going to have to do the tasks regardless of how difficult or how much time it takes.
I realize that so far I haven't done a good job in answering your question of how to train your brain.
- Before you start, make a checklist of all items
- Check for loosely defined or inconsistent requirements and ask for clarification
- Communicate any design issues... often designers do not think about "State X" or "Case B" until you bring it up... and sometimes that requires rethinking the design
- Before you commit/submit for review, you should review the requirements and checklist
- Make sure you have the right tools (Photoshop required to check pixel perfect alignment?)
It seems like you are in early in the project and that it is the first time that you worked with this designer. It will not take long to start to learn what they are looking for and where they are explicit or general.