Not true. The majority of the Eritrean people have been in the highlands for thousands of years. There is a noticeable difference between the unmixed Ethiopian/Eritrean gene and the Congolese gene. Here is a study where they address the unmixed Horn of African gene (Ethiopic), the unmixed Near East African gene (nilo-saharan), the unmixed West African gene and West Eurasian Admixture.
It shows how diverse Africa is and how of the West (niger-congo), Near East (Nilo-Saharan) and Horn of Africa (ethiopic) are very unique from one another.
Now as to where your mothers results might have came from. There is a group in Eritrea that migrated from West/Central Africa that resides in the Western regions.
Its very possible that this could be the case. In any case I hope it doesn't make you feel less Eritrean. Many African Ethnic groups migrated from east to west and vice versa. You are still Eritrean no matter what the tests may say.
Well, I guess I can just chalk it up to Ancestry's DNA test just not being very accurate; it's actually very general. They just say that "other small sampling from this region seem to share similar DNA" or something like that (I am paraphrasing.) This is the map of what they claim that part of my DNA is from:
For reference, here is a photo of my Mother in her Teens:
And as a young adult, on your left (both photos taken in Asmara):