A number of herbicides such as Classic, Reflex, Pinnacle, Basagran and Pursuit can damage soybean flowers. The labels of all these products caution about not spraying after flower initiation
The soybean plant produces more flowers than it needs so you have to weigh the merits of yield loss due to weeds versus yield loss due to knocking some flowers off.
Products that are safe after flower initiation include Venture, Assure and glyphosate. The issue with these products is surfactants (surface-active agents). Sometimes surfactants can affect bean flowers. The surfactants in main line glyphosate products Touchdown and Roundup are safe. If you are using a generic glyphosate ask your supplier if it is safe to spray soybeans in flower.
The main question is, will the weeds affect your crop?
If you have IP soys you have to get rid of nightshade and volunteer corn. If you have crusher beans and a few ragweeds you may have to live with them knowing that they may not cause that big a yield loss. Generally broadleaf weeds cause a bigger yield loss than grasses. In beans it is harder to control broadleaf weeds than grasses.
Finally, there is an herbicide residue concern. They are finding glyphosate in soybeans at harvest. Since the crusher bean of international commerce is Roundup Ready, this is not a big issue now. It may become larger in the future. But if glyphosate residues are found in soys it is realistic to expect there are residues of other herbicides as well. If the residues of other herbicides become an issue we may have to quit spraying soybeans earlier in the season. BF