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I'am using spacemacs and I was reading this 5.2.1 TODO keywords as workflow in the org manual and it says that to set a specific state right way the sequence of keys C-3 C-c C-t can be used.

If I hit the control key and the 3 key at the same time it shows me C-u 3- and I can't seem to figure out how to do it as C-3. It still works though. Should I just ignore this and remember it's the same or is there a way to type it as C-3?

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    You are seeing C-u 3- in the echo area because Emacs is interpreting your C-3 as a prefix argument. In that context it is the same as C-u 3, and the final hyphen lets you know that Emacs is waiting for more. It's waiting for a key sequence in order to look up its command and apply the prefix numeric argument (3) to that command while invoking it. – Drew Feb 9 '18 at 16:15
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Disclaimer: My answer pertains to vanilla Emacs features and default keybindings. The concepts should be the same in Spacemacs, but the default bindings may differ.

If I hit the control key and the 3 key at the same time it shows me C-u 3- and I can't seem to figure out how to do it as C-3. It still works though. Should I just ignore this and remember it's the same or is there a way to type it as C-3?

For most practical purposes they're the same thing, subject to the type of terminal you're on, i.e. how modifier keys are interpreted.

See (emacs) Arguments for the whole shebang, particularly the last paragraph:

   On graphical displays, ‘C-0’, ‘C-1’, etc. act the same as ‘M-0’,
‘M-1’, etc.

Note also the following distinction between plain C-u and numeric C-N/M-N (for some integer N) arguments:

   A few commands treat a plain ‘C-u’ differently from an ordinary
argument.  A few others may treat an argument of just a minus sign
differently from an argument of −1.  These unusual cases are described
when they come up; they exist to make an individual command more
convenient, and they are documented in that command’s documentation
string.

See also (elisp) Prefix Command Arguments for the nitty gritty details.

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