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Potentially, it could, if it means you were not able to establish good relationships with your professors or become involved in a research project. If you think your application is weak, you might want to take some time to strengthen it before you apply (work or volunteer to get more research experience or to get to know people so they'll write you good letters). Your question is a bit vague. If you did well at your schools, have reasons for transferring, and were still able to put together a strong undergraduate career, you should be OK. If it just looks like you lose interest in a place and move on after a short period of time, or if it looks as though you have trouble getting along with people and move to escape bad relationships within your department, it could be a problem for you.
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