There are a couple of recent tickets about lag.
I have noticed lag in 1.9b3. I had assumed it was Wine/Linux related but now I'm not so sure.
It is rare but sometimes the game will freeze for seconds. A recent example was undocking from Anton for the 'meet me in Silla' mission. the game froze for about 5 seconds.
All freezes have successfully cleared over time with no apparent effect on the game.
The key memory can also can lag. Often when scrolling/holding down a key the game will freeze for a period, usually less than a second, and when it starts again the key actions will then run in quick succession until caught up. Again no effect on the game.
Will take more notice of future glitches.
EDIT: Scrolling down the Ship's Cargo Hold dockscreen when lots of items are present shows a lag as the cursor scrolls over autons. Other items don't seem to cause lag.
Updated info.
The freeze when undocking from Anton is consistent and is related to total system count.
CC and TBR, node count 96, a small amount of freeze can be seen.
CC, TBR and Near Stars, node count 114, gives under a half second of freeze.
CC and the Network extension, 144 systems. gives around 5 seconds of freeze.
CC, NS and the Network extension, 162 systems, gives 20 seconds of freeze.
It might have something to do with intIsGateToSystem running inside intGetGateToSystem. This is the only node related code I can see in the mission.
Destroying Helena's wreck also causes freeze as does Jenna when she goes home. These run the same helper functions.