The Ancestry API can't tell that you already are using that source in RM. When adding a source make sure all the options are checked to add or update facts that are using it before Accepting Changes for the person. If the sources are identical then going to Lists>Source List>AutoMerge should merge them.
I took a few minutes to jot down the process I am currently using for completing the details for sources imported from Ancestry using WebHints. (The same basic steps can also be used to complete sources added using Tree Share.) This requires many (many-many) mouse clicks to accomplish but seems to do the best job I have found. I would appreciate any additional thoughts on how to make this method more efficient.
(It sounds worse than it really is, once you get used to the process.)
1 - Goto WebHints, determine new fact/event to be added to RM from A.com for a person, add the fact/event using the normal process.
2 - Highlight WebHint record in Record Hints and view on line in Ancestry (click view on line button).
3 - When Ancestry record screen appears, click Print button to display print preview screen.
4 - When print preview screen appears, highlight the record details including the source citation, source information, and original data. [Cntrl/C] to copy to clipboard. Close print preview screen, Ancestry record screen, and return to RM WebHints screen.
5 - Click the Edit RM person button and then highlight the Fact related to the source data saved. Double click on the source block for this fact to open the Citation Manager screen. Double click the source record being worked to open the Edit Source screen. Click on the Detail Text button to open the Research Notes screen. Click into the research notes field and use [Cntrl/V] to paste the source details into this field.
6 - Scroll down the Source Text to "Source Information" and highlight the Source Information and Original Data text. Use [Cntrl/X] to cut this text and place it on the clip board.
7 - Click on the Master Text button to open the Master Text - Source Text screen. Use [Cntrl/V] to paste the clip board into the Master Source Text field.
8 - Click on the Citation button to open the Edit Source - Citation screen. Edit the Master Source title field to insert the "user preferred" master source title prefix in this field. [Example - "1930 Unted States Federal Census" becomes "[CEN] 1930 Unted States Federal Census"]. Click OK button at bottom of screen. The focus will now return to the RM Edit Person screen. Edit the Description field for the Fact being worked if/as desired.
9. Repeat steps 1-9 for all facts/events to be added to a person from WebHints to RM.
Adding user preferred master source title prefixes as new source records are added to RM is more efficient than attempting to update them at a later time.
Use of master source name prefixes automatically groups the master source list by the prefix. This makes searching for similar or duplicate master source names easier, and helps facilitate the use of the merge tools to get rid of duplicates. The merging process can be completed any time after new master sources have been added to the list. It is usually done on a periodic, "housekeeping", schedule.