Is it a specific rule, or is it just down tuning things like AC and HP? Because lethality has been a recurring issue is basically all Paizo games I've run RAW.
core rules give advice how to adjust it, it really is just adding/removing another monster, rest stays the same (party size only matters during encounters, and xp reward doesn't change with size either). if it's a single enemy it might be a bit more tricky but usually it's ok to just bump it down a level or 2 and add some cannon fodder or a hazard as distraction while staying roughly with the budget. in general it's a good idea to have a few "equal" enemies than a single big one, in part in how saves and the action economy work - party of 4 has 12 actions, versus a single dude that has 3, so usually stats accommodate that to even it out. it's one of the reasons low-lvl casters suck a bit till around lvl 5-6 since they can't get over the saves reliably (and low-lvl groups don't have all the tools for (de)buffs either or know how to use them). one argument I read a few times is that fights against a single big bad feel more "epic", where my argument usually is it's not a videogame where most "bosses" sit in the last room waiting till the party clears out the trash, and usually not alone. if you consider the xp budget as a sum for a dungeon or area it gives you even more options, like combine some trash groups (depending how fast your group is with combat) or split them into lower level ones (which makes lower-level caster feel good too if they can just go ZAP MOTHAFUCKA and nuke a bunch of rats all at once with their AOE cantrips they don't get to use often and most do meh damage).
lethality comes down to the party (some suck at combat, some have the wrong combo of classes etc. - had a group without a fighter or other frontliner once, bit of a pain, but luckily only a oneshot) and GM experience and hard to put in RAW. some (AP) monsters are overtuned for example and the encounter setup itself made it harder than it should be (can't remember which one it was, I think frozen flame, but you get chased so not much time to heal up again etc.). and even a low threat encounter can be a pain in the ass depending how the dice roll #justd20things.
another trap that doesn't really get mentioned (maybe in the remaster) is lvl 3-4. pf2 works fine from level 0, but the game expects players to have to appropriate runes (which is something else I can't remember if it's mentioned explicitly, it's one of those things you know when you do somehow), the automatic bonus progression table lays it out if you don't want to bother with runes or equipment in general but what you "should" have. at level 4 players get striking runes which double their damage die, so most lvl4 monsters have the stats reflecting that. put them against a lvl3 party and it's harder than it should be. now add the first paragraph where some GMs possibly put a single lvl4 (or even lvl5) boss against a lvl3 party, and shit can get un-fun fast.
some other things that might cause issues: casters don't get "spell" runes (something people often complain about), my assumption is to keep them in line and require the rest of the group to work with them instead of being a one-man-show. depending what your groups expects, play and what they find fun you can always add that to make easier for them to overcome saves. blowing your prepared spell and constantly get fails can suck and feel like there's no real power progression - but I'd advice to slowly let them learn all the tools they have (even if it's just something simple like delay so the rest of the group can set up a trip etc), and worst case they can always use a hero point, which is something else you might wanna change and have it work more like 5e advantage than RAW - roll, fail, hero point, roll again, fails even harder, spell AND hero point blown for nothing sucks even more.
if you use the "proficiency without level" variant keep in mind you need to adjust some stuff. for some reason quite a few GMs I've seen pick that for a more "gritty" feel or because they come from 5e, and then forget to apply the adjustments for some reason. worse sometimes they don't even give out the equipment (like runes) the game expects (because again MUH GRITTY MUH LOW FANTASY) and then it gets even worse.
another thing regarding RAW, some parts of APs are written with a certain XP progression in mind, so they got lot of filler and possibly harder encounters simply to fill that XP quota. if you use milestone leveling you can cut/revamp quite a bit of that to make things go faster, both in terms of encounters and amount of sessions (or just fudge the xp you give out).
TLDR: apply the rules, they usually work, then apply flavor as needed.
EDIT: another thing you can do and
@Ghostse reminded me off: just give them an (and extra) animal companion or henchman they can control (if they want to since it's a bit more work for them), which you can fudge easier. like have command animal grand 3 actions (but then limit the amount how often you can command to not get it out of hand) or buff the companion etc. by giving him more intelligence so they can "act" smarter on their own for example.
bonus points if inject a beastmaster marathon beforehand.