The rear engine mount is notorious for loosening up on the Pre-Gen EX250, needs to be checked and re-torqued regularly.
Or, another thought is that your '07 is now 10 years old and I'm gonna guess you've probably never serviced the swing-arm pivot or the Uni-Shock linkage.
And the original rear shock, by KYB, is a really lousy piece of equipment (even when it was brand new) that could easily be going sour at 10 years of age.
Bottom line: this ticking/clicking issue is something that will probably go away if you do the long-term maintenance the bike requires.
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