I am not in the lab everyday. In fact, I am basically never in my own lab with the purpose of doing science. We can argue over whether that is the most effective way for things to get done, but it's the reality of my situation. As a result, I'm not there to see what people are up to all the time.
Once in a while I'll either get methods text for a paper or see something in lab meeting and wonder "why did you do it that way?". Inevitably the following conversation will take place:
Student: "The normal protocol wasn't working so I found a workaround."
Me: "Did you test the effectiveness of your new protocol against other variants of the conditions you changed?"
Student: "No, this worked so I went with it."
Me: "Did you try and figure out what wasn't working for you with the old protocol."
Student: "Um, not really..."
Me: "Are you the only one using the changed protocol?"
Student: "No, I gave it to Undergrad X and Y."
I don't mind people trying to improve protocols in a systematic way, nor do I discourage people from troubleshooting lab issues. However, changing established protocols in a haphazard way and propagating those changes to others is the stuff that drives PIs crazy. Not only is it bad science, but there is enormous potential for unanticipated downstream issues. If you alter the concentration of reagent A in Part 1 of a protocol and it effects downstream process 4, it is entirely possible that a lot of time will be spent troubleshooting process 4 before the change to reagent A is mentioned and the link is made.
Even minor "tweaks" to a protocol have a way of propagating until one day the PI goes to read the methods for Standard Procedure One and it turns out that the game of lab telephone has turned it into Stendard Progressional Ounce.
Lab protocols can be changed, but systematically, and with everyone in the loop so that people are aware of the changes and all working from the same playbook.