The counter on the application’s badge does not seem to be correct

Counts that you see within the app or on top of the app's icon are determined at runtime, and so these should always correctly reflect the total and tally against the counts you see everywhere else within the app. There's a very slim chance of these counts being incorrect. 

There is however a subtle difference between the counts you see within the app and the one you see on the app's icon. Normally you wouldn't ever see any difference between the two, however in case you have selected certain lists to be Excluded from Today or All (right click on a list to get to these options), the app may present you with a different number within the app (since tasks from those lists aren't included in the count) but a totally different count may display on top of the app's icon.

The reason for this is obvious: 2Do's main job is to keep you on track. You may have several tasks that are now overdue within lists that are otherwise hidden from showing under All and Today. We still don't want you to miss out on these, and so the counter on the app's badge will show you the correct count, of all such tasks. 

Another setting that may influence the count are Include starred tasks in Today. You may wish to inspect your preferences and options and if still in doubt, please contact us and we'll try our best to help.