It's clear from the material I've read that people were aware of the Spanish Flu (sometimes referred to as "La Grippe" in Europe). Given that the flu's transmission was perhaps helped spread by troop movements, I'm wondering whether or not any of the militaries participating in WW1 had any protocol for helping the minimize infection among their troops. Certainly, there are photos of large wards set up among the civilian population in old gymnasiums and the like. Given that the flu attacked younger adults with stronger immune systems, I imagine it would be a big concern for any army.
The book The Great Influenza is a good read and deals quite a bit on this matter.
It has been a bit since I read the book but from what I recall there was some people pushing for large quarantines, but largely the commanding elements of the US and Canadian Militaries did not listen. Opting instead to continue shuffling troops between bases, which accelerated the spread.
http://www.amazon.com/The-Great-Influenza-Deadliest-Pandemic/dp/0143036491