In X, you have N selections referenced by atom. Two atoms (PRIMARY and CLIPBOARD) are sometimes used interchangeably by various software, leading to all sorts of shenanigans where for example selecting then middle clicking pastes something that was "Ctrl+Ced" elsewhere or vice versa.

Additionally, X selections aren't buffers - they're handles used asynchronously. So, when you paste, if the source application is dead or has mis-handled its state internally, you don't get what you expect.

These behaviors are patched over by clipboard managers which manage PRIMARY and CLIPBOARD interactions and which immediately copy the selection into a buffer to make it long-lived. However, each desktop environment's clipboard manager has gradually expanded to include all kinds of strange environment-specific metadata possibilities (to enable, i.e. "Paste Special" options from a spreadsheet).