The number on a blue background next to the word “flags” is the number of outstanding flags that are shown. For a 10k user who is not a ♦ moderator, these are the canned flags on posts such as “does not belong here”, “not an answer”, etc. If you take an action on a flag, or if a moderator dismisses a flag, or if the flag is dismissed automatically (e.g. because the post is deleted). If you wonder what to do with these flags, please read Which actions using the 10k-moderator-tools do really help the diamond moderators?
From a /tools
page, if you click on the review
tab, you're brought to the /review
page. When you reach 10k rep, that page receives an additional tab which shows all the pending suggested edits. The number on a dark orange background is the number of pending suggested edits.
The same numbers¹ appear on the top bar in every page: the number of flags on light orange to the left of the tools
link, and the number of pending edits on dark orange to the right. The flag indicator isn't shown if you've viewed the flag list recently. The number of suggested edits isn't shown if it's less than 5. (This is for Stack Overflow, the rules are slightly different on sites with less volume.)
¹
My screenshots show different numbers because they were taken at different times.