An easy way to avoid this error when submitting feeds to campaigns is to use the Feed Filter Options combined with the Automatic Submit Feature.
I have about 10,000 keywords per feed creating 10,000 AdGroups. This exceeds the Google API limit of 1000 AdGroups per submission.
In order to skirt this issue I set the Feed Filter at 1 - 1000 on the first day. Then after the first automatic submission I change the value by 1000 (1000 - 2000, 2000 - 3000 etc.) on each subsequent day for 10 days till all the keywords in the feed have been submitted and all the AdGroups have been created.
Works for me.
Ad-Groups count exceeded 1000