The worst ones are diagrams that look clean but hide all the decisions that actually matter. A messy diagram that shows the real tradeoffs is more useful than a pretty one that lies
Once worked with a systems architect who intentionally disorganized their flow diagrams by just moving nodes in their flow to random places (hi Dan!). The only reason I can think of why he'd do that is to maintain job security by keeping the junior apps folk confused.
The Slack notification flowchart is an old favorite: https://slack.engineering/reducing-slacks-memory-footprint/
It amazes me that they are spending all of this time reducing the memory footprint and not do the most obvious thing - just stop using fucking Electron