Agreed, it's out of hand, but playing with a more informed idea of how things work is clearly going to help you with some of your diplomacy problems. You've obviously picked up not to walk in their lands without securing military access... so put it hard to work now.
Btw the reason for this upsetting them (which you called into question) is quite natural if you consider yourself as the ruler of a nation. Primarily, it's that it makes you nervous as hell when a neighboring country brings a friggin army onto your sovereign lands!!! It can easily be the precursor to a full scale invasion, and just isn't polite to boot. If you would allow the computer to do this to you with how little it respects alliances... then you need your head examined, b/c they'd definitely try to gobble up some underguarded central province of yours while they seemingly wander around aimlessly. I can see it already:
French commander, landing at England: Hello there!
English commander: Well hello. What are you doing here?
French commander: Well, we thought it would be a nice day to go sailing.
English commander: ...and land heavy infantry?
French commander: Oui. We find it most comfortable to travel with our heavy armour and weapons on. After such a wonderful voyage, it only seemed appropriate to take a nice peaceful stroll through the woods to see... where was it I said we were supposed to be going today?
French flunky: To Scotland, sir!
French commander: Yes, we're going to see Scotland. Most of the men have never seen it. I hear it's beautiful this time of year.
English commander: Oh yes, quite beautiful. Full of... hills. And goats. Yeah. Very well men, let them pass!
*French army lays siege to London*
English commander: BLAST!!! They said they were going to Scotland, and I believed them! FRIGGIN FROGS!!!!!!!!!
I'm sure you get the point.
In other news, It's wise to avoid making aggressive moves on factions that have high pope-o-meter ratings, as it seems when I've done so it causes substantially worse hits to my pope-o-meter, and is seemingly more likely to draw sanctions as well. It helps to have a very high pope rating yourself as he messes with you less. Sending a diplomat to tribute him dough and building big-ass church buildings are good ways to help this along. Of course it's also nice to have a pope from your country, so actively training up priests to become cardinals and control the college of cardinals that way can be amazingly useful to this end too.
I would also strongly advise against making alliances with any faction you intend to wage war with relatively soon, as breaking those alliances really makes your reputation plummet. If you do find yourself in a situation where you want to start a war with an ally, the least damaging bet is to try to draw them into attacking you. I don't know if actively trying to piss them off hurts pope rating or global reputation, but if not then for instance military trespassing would definitely be a good plan. I don't believe assassins trigger war either, and they do seem quite effective at sinking those relations.
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