Hi,

The method org-agenda-show-clocking-issues has a faulty regex, which 
leads to false-positive
clocking issues: " Clocked: +(-\\|\\([0-9]+:[0-9]+\\))"

There is no outer group to limit the OR-expression \\|, so the right 
half will match timestamps with
a closing parenthesis without any "Clocked" in front of it.

I added a non-capturing group in the attached patch: " Clocked: 
+(\\(?:-\\|\\([0-9]+:[0-9]+\\)\\))".


Reproduction:

Define a custom agenda:
(setq org-agenda-custom-commands '(("d" "Clock report for today" agenda ""
                                     ((org-agenda-span 1)
(org-agenda-start-with-clockreport-mode t)
                                      (org-agenda-start-with-log-mode 
'clockcheck)))))

Use an org file that is included in org-agenda-files, and add this 
sample headline:
Sample headline with time and closing parenthesis in it (it happened at 
12:00)

Clock in and out of the headline, make sure the clock timespan is at 
least 1 minute, and open the
agenda defined above. Observe that the headline is reported as 
overlapping with itself, as the
faulty regex will match twice on its agenda line.

Best Regards,
Tim