The tourists won the final game to lose the series 2-1, and the teams are now preparing for a three-match Twenty20 series, starting on Thursday.
"We constantly talk about not giving easy boundaries. That's an area we can get better at," Bayliss told BBC Sport.
"We didn't bowl enough balls in the right area."
England conceded 356 runs in the first match of the series and 381 in the second, but restricted the hosts to 316 as they secured a five-run victory on Sunday.
"The bowling was a little disappointing in these three games," added Bayliss. "The guys would be the first to admit that.
"But we have seen them bowl well in the past so there's no reason why they can't bowl well going forward.
"On Sunday, on a helpful wicket, if we'd got the ball in the right areas more often I don't think the result would have been so close."
Seamer David Willey could play in the T20 series, despite a shoulder injury.
The 26-year-old seamer was injured on Sunday, but a scan has revealed there is no significant damage.
England will host the 2017 Champions Trophy this summer, and Bayliss has not ruled out Stuart Broad returning to the one-day team.
The Nottinghamshire all-rounder, 30, has recently been used as a Test specialist.
Bayliss said: "There's probably two or three players on the outside looking to get back in."
Thursday, 26 January in Kanpur (11:00 GMT)
Sunday, 29 January in Nagpur (13:30 GMT)
Wednesday, 1 February in Bangalore (13:30 GMT)
England's bowling during their one-day international series defeat in India was "a little disappointing", says coach Trevor Bayliss.