I assume the problem is focus and not camera shake given the flash should freeze motion pretty well.
Without sufficient light and contrast your camera will not autofocus. Most flash units will have a focus assist that draws bright red lines on the subject, allowing for a contrast the camera can focus on. This will only work when your Canon camera is in one shot focus mode (do not confuse with the drive mode). If in AI Servo mode, the flash focus assist will not work. The flash focus also has a limited range -check the flash manual. to set focus modes you'll need to be in a "creative" mode such as Av, Tv, or M. (Not the green rectangle mode)
Is the camera in one of the creative modes? Such as Av, Tv, or M? You'll need to use one of those modes so you can set the camera to use one focal point. Center point is best. You'll see the focal point as a red rectangle when you autofocus. What your manual may not tell you is the camera is actually focusing on an area at least twice as wide as the rectangle you see. If it finds something more contrasty in the back ground -even outside the red box but close, it will choose the higher contrast object for focus. Select center point focus and be aware of other higher contrast light just outside the focus rectangle.
In very low light, you may just have to use manual focus. Some more expense lenses have distance scales so you can focus by approximate distance, but I hate answers that tell you to buy different stuff. Your eye can focus better at lower light than the camera can. Look for anything on or near the bat with a glare or shine and adjust focus until that glare or shine is minimized. Otherwise look for a line that you can judge is sharper or not.
A final option is to cheat. Get a friend or a light source you can aim and leave in place to provide extra light for focus. The flash will overpower it, so it won't show much in your final image. Otherwise, autofocus with the camera on a tripod while the light source is on, them turn off autofocus and the light source before taking your shot. In this case you could even forego the flash, set for ISO 125 and take a long exposure -assuming the bat and the tree aren't moving. You may find the natural light is more interesting. -Or cheat and set a light source at an interesting angle on the bat! (I once used truck headlights to illuminate a news photograph of a police armored vehicle on a dark country road.)
Summary: Av or M mode, one shot focus or manual focus, center point focus, look for contrast or lines to focus on, add light even if only during focusing.
I love night photography without flash. Lots of interesting light. Good luck.