At Sullivan's before the fight, Seamus tells the Doctor that he broke the fifth commandment (Thou shalt not kill) and was told to give ten hail Mary's and call him in the morning. Though murder would normally warrant a harsher penance, the Doctor was simply brushing Seamus off with a variation on the old chestnut "Take two and call me in the morning."
When Janeway says "Maybe I'll stop by the pub," it has clearly been dubbed. Kate Mulgrew clearly says a word other than "pub."
Several crew members sustain minor injuries during a pub brawl in the holodeck. However, unless they've been specifically disabled, it's well established that the holodeck's built-in safety protocols would prevent any such injuries from occurring.
Chakotay sees Michael Sullivan after Janeway changed Sullivan's character profile. Chakotay says "I don't think we've met before." Later on the bridge Chakotay mentioned Sullivan being taller than he remembers, which would suggest they have met before.