Apply etch resist on copper
I've had the same problem with toner transfers and have given up on them.  One tip is "Not all toner is the same".  I use both Brother and Canon laser printers, OEM and after market toner, etc. and never could get a good transfer.

So what is the solution?  I've found the photoresist dry film to be a great alternative.  I'm still learning exposure times, etc., but it's certainly better than the toner transfer, especially when the toner transfer just doesn't work.

The photoresist dry film can be purchased in rolls or even in pre-coated PCBs.

The process for the film goes something like this:


Clean the copper clad PCB with warm water, soap, and the non-metallic scouring side of a dish sponge.
Cut a piece of the film a little larger than the PCB, then use Scotch tape to peel off the backing paper.  Look for some Youtube videos and you'll see this demonstrated.
Don't touch the film where you just removed the clear backing paper from.  Begin applying it to the PCB, starting from one end of the PCB and gently lowering it onto the PCB while working out any air bubbles as you go.
Once you have done this, make sure the film laps over one end of the PCB then feed it into a laminator.  I've seen some people use an iron for this, but I had access to a laminator.  Feed it through a few times and that should be good.
Print the board design on transparency film.  You can get transparency film for either Inkjet or Laser printers. Make sure you print at least a couple of copies of the layout, because you're going to need to stack them.
Cut out the layouts and carefully align them on top of one another.  This Youtube video explains the reason why and is a good tutorial for photoresist etching (minus the annoying computer voice): https://youtu.be/UsmE1gLbHqI
Get a piece of glass or plexiglass that does NOT have a UV protective coating on it.  You can borrow the glass from a picture frame.  place the layout on the piece of glass, then place the PCB with the photoresist film on top of it, aligning it carefully.  Tape that to the piece of glass and you're ready for exposure.
I recommend using sunlight because it's fast and effective.  I haven't pinned down the best exposure time yet, but 5 minutes over exposed it.  Over exposure will make it to where the un-exposed parts become slightly exposed and the film won't come off where it's supposed to come off at during developing.  Over exposure doesn't hurt the exposed part of the film.
Develop it using water and baking soda (or Sodium Carbonate).  The tutorial I linked above explains this part.
Etch your board like you would with the toner transfer method.
After etching, remove the photoresist film from the PCB.  You MUST use Sodium Hydroxide to remove it.  I tried Acetone and even Lacquer Thinner and nether one had effect.  This video demonstrates this process: https://youtu.be/cRCFGZxmob0  You'll want to have the Sodium Hydroxide on hand before you begin, because you can't get the film off if you make a mistake.


You can also use the photoresist film to make a solder mask, which I thought was pretty neat.

I certainly think this method is the best one since the toner transfer failed no matter how many times I tried.  The materials you need are inexpensive and easily found.  I hope this helps.