If all executive powers is held by the President and FBI agents can make arrests, doesn’t that mean the President can too?
Any individual in the US — including the president — can make a citizen's arrest for certain crimes committed in their presence.
That aside, the power to make an arrest is vested in certain official positions. These positions are established by federal, state, or local statute — i.e., by Congress, state legislatures, or local committees — and individuals are explicitly granted the power when they take these offices, for the term they hold such offices. This includes police, federal agents, and certain other people who are not conventionally thought of as 'office holders' (despite the fact that they are government employees we typically call 'officers'). However, the power to arrest is not explicitly granted to the Office of the President by the constitution or by Congress, so the US president has no more power to personally arrest someone than any regular person does. Even though the president is titular head of various federal agencies whose officers and agents are empowered to make arrests, the power itself does not 'percolate' upward, but remains attached to the offices themselves.
In fact, under normal institutional constraints US presidents do not even have the power to command federal or local law enforcement to make arrests. That power is held by chiefs of police, sheriffs, and the heads of federal agencies with law enforcement powers (as granted by Congress or other legislative bodies), and is exercised independently of the White House. This is an intentional separation of powers, meant to prevent the chief executive from using law enforcement against political opponents, opposition journalists, or anti-administration activists. Those institutional norms suffered under the Trump administration, and are ignored or objected to by some of his most vehement supporters (who still call for mass arrests of their political opponents), but they may be recovering under the Biden administration.