The U.S. has also taken part in clandestine operations aimed at Iran and its ally Syria. A by-product of these activities has been the bolstering of Sunni extremist groups that espouse a militant vision of Islam and are hostile to America and sympathetic to Al Qaeda."
"By-product" in this usage means an unintended consequence. Weakening Assad benefited many, including ISIS but it wasn't intended to help them.
by·prod·uct
ˈbīˌprädəkt/
noun
noun:
by-product
an incidental or secondary product made in the manufacture or synthesis of something else.
"zinc is a byproduct of the glazing process"
a secondary result, unintended but inevitably produced in doing or producing something else.
"he saw poverty as the byproduct of colonial prosperity"