1999 Chrysler Sebring slight hesitation

Both the transmission and engine can cause a hesitation you'll need to rule out one. It is easier for me to check the engine and rule it out first. If your able to duplicate the hesitation in park I would suspect the engine if does not I would suspect the transmission. If the hesitation only occurs when in 4th gear at 48mph it would send up a red flag that the issue is with the transmission.
Check the transmission fluid level that it is correct and not contaminated or aerated.
These transmissions have a computer just for the transmission and another computer for the engine. When the batter is disconnected or almost anything replaced on the transmission will have to go through a shift quality relearn. What that means is the transmission computer takes input from the driver and all the sensors and creates a data base to improve transmission shifting to make it more effective and comfortable.
Driving the car will give more time to improve the issue or allow the computers to detect if there is a issue with the engine or transmission.

Warranty, even better! Take the vehicle back this is not normal.

Does this hesitation only happen at a certain speed or can you get a hesitation to happen if you rev the engine (in park) to a certain RPM range?
During the transmission repair did the torque converter get replaced?
Do you access to a scan tool that can access the transmission control module to check for any fault code stored?
Let me know