These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Squick: The descriptions of the surgery Pepys underwent in 1657 to remove a bladder stone will set your teeth on edge.
Medical experts who have read the diary, in particular the parts including Pepys's sympathetic descriptions of his wife's health troubles, conclude that she suffered from Bartholin's cysts. (You can look it up on That Other Wiki, but be aware — the included photograph is Not Safe for Work.)
The surgeon's own papers show that he'd very recently purchased a new operating knife, and Pepys was probably the first person he used it on. As such knives were never sterilised, this is probably why Pepys had a good recovery.
Values Dissonance: Pepys casually mentions things like beating up his household servants.