When Kirk and Spock shoot the Horta with their phasers, nothing appears to happen, and the Horta backs off into a tunnel it creates. Kirk and Spock run over to the new tunnel, across a floor that is clean. When the shot shifts to show them from the tunnel, there is a piece of the Horta on the floor (to the left) where there was none before (in the previous shot). When the view shifts back to showing the chamber they are in, the piece of the Horta is on the floor.
When Kirk and the Horta have squared off against each other, and Spock enters, there's a two-angle back-and-forth. When the camera is directly at Kirk, he is kneeling with a phaser in his right hand. When the angle switches to Kirk at left, Spock far center, Kirk is kneeling but with a communicator in his left hand. The change goes back and forth a couple of times.
Using clubs to attack the Horta would make no logical sense. Since the Horta exudes an extremely corrosive fluid to create its tunnels, capable of dissolving large quantities of solid rock in seconds, all it would need to do to protect against the clubs is release a large quantity of the corrosive. Any kind of club used to attack the Horta at that point would simply disintegrate when it touched the corrosive on the Horta's exterior.
After Spock's initial mind-meld with the Horta, Kirk and Spock discuss asking the Horta where the 'Retardation mechanism' (for the main reactor) is. There is never any indication that they knew the mechanism was cut out and not simply dissolved away by the Horta. Nor is there any logical reason why the Horta would keep and not just destroy the reactor pump, if it wished to drive them off the planet.
When Kirk and Spock shoot the creature after seeing it for the first time it retreats into a tunnel. The tunnel has a flat bottom as it moves away but in the next shot from the reverse angle it has a rounded bottom.
The goof item below may give away important plot points.
If there have been many generations of Horta on the planet, and each generation is 50,000 years, that means they have been on the planet for many thousands (perhaps millions) of years. Since they digest or move through solid rock by using extremely strong corrosives, two things should result from the existence of many thousands of Horta over the course of time: 1. The result of the corrosives dissolving rock should be extremely large quantities of polluting gases that would have poisoned the atmosphere long before humanoids arrived on the planet, making it too difficult for the miners to mine the minerals (the Horta would be unaffected by the 'polluted' atmosphere). 2. The result of all the tunneling by thousands of Horta over that length of time should have depleted their "food supply" planet, as there is no natural process on the planet that would replenish its supply of 'rock'.