It is possible and usually expected for a single gene/gene product to be associated with more than one GO term. The fact that you may have found that there are two or more different GO terms associated with a single gene/gene product in your results should not be a cause for concern.
The Gene Ontology allows users to describe a gene/gene product in detail, considering three main aspects: its molecular function, the biological process in which it participates, and its cellular location.
For example, the homeobox D9a gene product from zebrafish has numerous GO terms associated with it. Each term describes details about this gene’s molecular function, localization in the cell, or its involvement in certain biological processes. One GO term explains that this gene product carries out the molecular function of selectively interacting with DNA (DNA binding), while a different GO term explains that this gene product is found in the nucleus of the cell.
Trying to write one single term that describes in detail everything about a gene/gene product in a single statement would require the existence of as many terms as genes there are - for all species - in the planet. This would be very unpractical and not easily scalable. Instead, the use of ontologies help us organize information in a way that allows researchers to use the same term to describe a characteristic that is shared by more than one gene product (e.g. all the genes involved in the process ‘translation’), and more than one term to describe all the characteristics of each gene product, as in the example above. This is a reason why you would see more than one GO term associated to a single gene/gene product.