This will only cause a problem if you are not prepared for it. It is not unusual for partners and spouses to have different credit scores, especially in the early years of being together. Buying a home together means that both of you will need to be open with each other about how each of you handle credit. You do not want to wait until you are about to close on a home to find out that the other person has such a poor credit score that there will be a delay in obtaining financing. So, both of you should get your credit reports now and share the information with each other.
When two people want to purchase a home together, married or as partners, the lenders will look at both credit reports. They are not only looking at the credit score, but also how much debt both parties have, how much income each person is making, how much is held in savings, and the size of the down payment. A large down payment can make lenders much more amenable to loaning money. Also, if the person who is making the largest portion of the family income has the best credit score, it is a positive.
The problem comes with a small down payment, high debts for both parties, and the person who makes the most income having the worst credit score. Lenders may suggest that only the person with the high credit score take out the loan, but that can cause problems with what name goes on the title. Most lenders only want to have the names of those who are taking out the loan on the title. Spouses or partners whose names are not on the title may have problems asserting their right to the property in certain circumstances. While the law has some protections for those legally married, this is not the best solution.
A better solution is to continue to shop for a lender that will provide a mortgage. Expect that it will take more time than anticipated to find a lender who will work with you, and you probably will be paying a higher interest rate on the loan. It may be more financially feasible for you and your partner to put off buying a home right away and take the time to clear up debts, work on building up your credit score, and save for a larger downpayment.