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It's become widespread practice among terminal emulators to filter out most control characters when pasting text from the clipboard to the terminal (e.g., xterm, gnome-terminal), to somewhat reduce the risk of text pasted from an untrusted source having unexpected effects.
PuTTY now does the same as xterm by default; that is, PuTTY filters out control characters other than CR, LF, tab, backspace, and DEL. There's an option to allow control characters (as previously), since they have their uses.
Note that this doesn't, in general, close the loophole when copying text from websites that what ends up in your clipboard may not resemble what it looked like you were selecting; there is still plenty of scope for mischief; see for instance this demonstration. (However, PuTTY does now prevent escaping from bracketed-paste mode, when enabled, as mentioned on that page.)