This is a rather specific problem.
But I couldn't find mention of it anywhere.
The MacOS terminal implementation has difficulty when the window, or more precisely the amount of data stored in the terminal process, gets very large ...
... say you've been using it for days, and lots of output has scrolled up, but you haven't opened a new terminal window ... maybe because you want to look at what you've done already. You could export it, but then you'd have to think about where to put that exported data.
Mac terminal tends to be a bit greedy of RAM, and if you have lots of these terminal windows, managing lots of projects, you may see some performance degradation.
... but, also, you may see some actual problems.
For example, if one of these terminals is connected to a remote host using ssh, and you start to use a visual editor (say, emacs, vi, or vim) on the remote machine, the editor might start to make errors, and become essentially unusable. The remote editor has expectations for terminal text control signals, and Mac terminal, unable to work fast enough or buffer signals reliably, because of the large volume of text in the current process, simply fails to keep sync.
So, you're not crazy. Not everything in computing is deterministic, especially when networking is involved. (And yes, Apple could and should fix this problem.)
For now, simply close the remote host, export the terminal text, close the terminal, and open a new one.