Hey there, sorry for the trouble! So, there's a number of potential things going on...

First, we put "sticky friction" on certain actions in the game (like killing enemies and getting hit), where the game pauses for a brief moment to give these actions more *punch*. Most people like this, but some don't... we didn't expose an option for this, but if you want to manually turn it off you can do so by editing your options file and changing the number in the following line to 0:

"m_stickyFrictionMultiplier": 1.0,

You can find your options files in the save directory, they should be named something like SlotA.options:

Windows: %USERPROFILE%/AppData/LocalLow/Dodge Roll/Enter the Gungeon
OSX: ~/Library/Application Support/Dodge Roll/Enter the Gungeon
Linux: ~/.config/unity3d/Dodge Roll/Enter the Gungeon

Second, one of the downsides of the engine we use (Unity) is its garbage collector... we've worked hard to obscure this and do this as little as possible, but sometimes the game needs to pause for a brief moment to free up garbage memory generated during normal gameplay. We attempt to do this on room transitions if we can detect that a garbage collection spike is near, since we'd much prefer these happen out of combat, but in particularly dense combat these can sometimes happen. Unfortunately the best solution to this is more RAM or a faster CPU, but if you already have a pretty recent PC, this isn't likely to make a noticeable difference. We're continuing to try to minimize this, and future Unity upgrades should also improve this!

Those are the first two things that come to mind. Without seeing exactly what you're experiencing, it's hard to say for certain if there's some other problem going on. If the sticky friction doesn't help and the garbage collection doesn't sound like what you're seeing, please let me know!