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02 Honda Civic EP3/SiR
I noticed the coolant was a bit low, asked the shop to top it up while it was in the other day. The manual indicates to use Honda Coolant/Anti-Freeze Type 2 part # OL999-9011 only, which is blue. I specifically asked the shop to use the Honda coolant specified for this car.
The stuff they put in is green. Is this wrong fluid was the color of the fluid just changed at some point?
While color is not the most important part. Ingredients are very important for example Mercedes BMW and Honda use blue coolant, the ingredients of each are different. You should always ask for the empty bottles of oils/coolants that are put in your car and check if they match the requirements of the car manufacturer.
The Honda Type 2 Coolant contains "NO Silicate and borates," and that is the key. What they probably used was the cheap Prestone from Walmart. Now, that's a pretty good coolant nowadays, but the chemical composition is slightly different. Will it have an impact? Hard to say, probably minimal. Your biggest risk is warranty compliance, but seeing as how you're driving a 2002 Civic, it's unlikely a concern.
Search the MSDS sheets to see the contents of the coolant. Note that the Prestone doesn't appear to have the KOH and it's unclear about borates restricted in the Honda fluid:
Prestone 50/50 prediluted engine coolant:
My recommendation is to not worry about it because the vast majority of your coolant is still the Honda Type 2 and the little bit they added to top it off is not going to vastly change the composition of your coolant. For other maintenance reasons, you may want to consider draining and refilling your coolant on a car that is 17 years old as that itself will likely prolong the life of your cooling components. In that case, just get the right amount of Honda Type 2 and take it with you to the shop.
Also,
More generally, why are coolants different? The composition of these chemical compounds is based on Society of Automotive Engineer requirements to maintain the viability of internal engine components. As there is a range of manufacturing metallurgy and composite components in the world, there is a range of antifreeze requirements.
They shouldn't have put green antifreeze in. The reason for this is that even if they flush it, it will work but green antifreeze isn't long-life like the factory antifreeze is. They used it because it's cheap. There shouldn't be any complications as long as they flushed the system first but it will only last three years instead of five. My own Veloster has green antifreeze in it because it had its rad changed before I bought it. The original Hyundai coolant wasn't green but it's worked fine for the past few years and I'll be replacing it with Global Yellow this year.
What that shop SHOULD have put in your engine is either Honda-Type (Not necessarily FROM Honda but Honda-Type) or Global Yellow. Either of those would work just fine and would last the same five years as the factory antifreeze.
