This is actually an old bug that has been covered in #2053 but it happens it's back.
Basically, when you connect 2 different fluid networks, the fluid type of one of the network will get replaced with the fluid type of the other, enabling a massive fluid exploit (creating lithium from water for example).

Oops sorry, it's not exactly the same bug as #2053 but it's still a bug on its own.

As you may have guess already, it affects gases too. When 2 gas networks merge, one gas is replaced by the other.

Yeah, this bug sucks, I've tried to come up with ways to prevent it but there's always some kind of workaround. TE handles this by having pipes of different fluid types simply not connect, but I'm not a big fan of that kind of functionality. I'm thinking that I'll incorporate some method to have the pipe drop on placement if two adjacent networks have differing fluid types.

Wasn't that the previous pressurized tubes behaviour? That is, preventing having 2 different networks close to each other.
Another idea could be setting colours on parts of the network to prevent any merge (something similar to logistical transporters). While it doesn't solve all the issues, it gives the player some control over his network.
Or maybe a filtering system. Once a network has been set to a given type of fluid, it won't be able to connect any other filtered network. Pretty much the same idea as colours but applied to the whole network. I was thinking of this since I read somewhere a Mekanism transportation block (sort of Dimensional Transceiver/Tesseract) was considered. Without a filtering system, teleport is almost out of reach imho. This would then require a manual purge of the network to change its fluid/gas type, which can also be a real pain.
I wish I could help more but none of those ideas are very sexy :(

My compromise is that the first fluid/gas type found in a list of transmitters is set as the primary type, and all other types of fluids/gases are ignored. Hopefully I can make this better in the near future.