Captain Bowman (B) and First Lieutenant Kayser (B) apparently hated each other bitterly. Both were court-martialed because of incidents arising from that hatred.
When John Hamill was court martialed, he complained that Benjamin Tayman blocked an order restoring him to duty, "through malice more toward some other officers of the Regt than towards myself, but because they sided with me".
In June 1862, rumors had the commissioned officers nearly in open mutiny, with the regiment reduced to 400 men, and Colonel Gregory being too harsh to the regiment and too lenient to the Confederates. The commissioned officers took those rumors seriously enough to publish a "card" denying them. They claimed, "we venture to assert that we believe there is no regiment in the service whose officers agree better, or have less difference of opinion." Less than a month later Bowman struck Kayser.
According to a report from 1903, the regiment was split when it was founded, between religious men and others. Colonel Gregory headed the religious men, members of the Young Men's Christian Association or other religious organizations, while Eli Sellers came to head the others. This split allegedly cause "considerable friction". JHR Storey (who served in the 109th PA) claimed that Sellers admitted to him in 1903 that he "got even with" "those Christian Association fellows in our regiment", whom he called "Gregory's pets". "[W]hen I got the chance I downed them, and when I became lieutenant-colonel I did get it", Sellers claimed. One of those men was Thomas Walter, whom Sellers insisted on ordering to lead a detail when Walter claimed he was unable because of his health to perform his duty; Sellers prosecuted Walter, who was cashiered from the army. (JHR Storey, [letter to President Roosevelt], 3 February 1903, transcribed in 'Thomas F. Walter', Senate Report 3309, 59th Congress, 1st Session, in Serial Set, volume 4905 F (session volume F))
Benjamin Tayman may have been caught in a higher-level conflict. According to General Humphreys, General Tyler made "false accusations against him [sc. Tayman] in connection with the battle of Chancellorsville". Humphreys claims that Tyler made these accusations because he knew that Humphreys had a "good opinion" of Tayman, and Tayman had "great regard" for Humphreys. (According to the regiment's consolidated morning reports, Tayman was under arrest by order of General Tyler beginning 13 May 1863, and on 11 June 1863, the Corps Commander, Major General Sykes, ordered Tayman "honorably released and restored to duty".) (See Henry H. Humphreys, Andrew Atkinson Humphreys: a biography (Philadelphia: The John C Winston Co., 1924), pages 265-267.)