Only in provinces where you are facing Mist Walkers and Rangers will the enemies have an advantage on initiative. For all the other provinces it pretty much goes both ways.
The first fighter you select is always placed in the middle, the second fighter to his left, the third to his right, the fourth at the top of the screen and the fifth and the bottom of the screen. Placing you fighters in the best possible position can make a huge difference in almost every fight.
True indeed, I always place my troops where I want them when attacking the enemies, the game will almost always place them in bad spots.
This only happens when the enemy has larger squads than the player. It is advisable to scout only the amount of provinces needed to unlock the next chapter in the research tree. The cost for fighting and negotiating to complete a province will increase with each newly scouted province. If a player stays within the number of provinces necessary to unlock the next chapters chest, most of the fights will be on a medium difficulty level or under, with maybe just a one or two hard provinces.
A quick refresh of the game will almost always fix that problem. If you find you are having this issue more often than not, you may need to clear your browser's cache or try a different browser.