Hello,
I had installed 5/8" engineered hickory wood floor 1 year ago. I had replaced the subfloor with 1 1/8" plywood with some hard work to make it entirely silent: fixing bad joists, glue, screws (the old wood plant subfloor was terrible).
My original desire was for a double glue down installation, with an underlayment glued to the subfloor and wood. I wanted silence above and from the living space below. The installer, and supplier convinced me to instead go with nailed cleats through a thin rubber underlayment ("glue down is for concrete"). I was worried this would be trouble, but the assurance of the manufacturer and a price tag of less than half led to my decision.

Sure enough there are three locations with a few boards that within months almost always make pop click noises when stepped on.
One problem area was an accidental low spot, that the installer first layered tar paper and underlayment to build up. There is no way to get under this section.
The next two areas could be accessed below from crawlspace. I suspect one of these is at a subfloor seam that was installed too-tightly (seasonal buckling).

What ways should I consider for fixing this?
I've contemplated removal and double glue down of trouble areas, injecting glue, or driving screws up from beneath.

If you do not mind a couple of putty spots on the surface, I recommend using a couple of the cleats nailed into the soft grain, the darker part of the grain, toe-nailed into the sub-floor right where the squeak or pop is. Cleats hold really well. You can pre-drill a small hole the width of a cleat to help with driving it. Set the cleat below the surface with a slotted screw driver, then use colored putty to match.

You can totally glue down over plywood - glue down is not just for concrete only. I've done a lot of high end custom homes and I always glue down long and wide engineered planks - if fact, I recommend it strongly when the price of the hardwood is high, since you've almost always got picky customers at that point and a full spread glue down install will cut your problems in half if done correctly. Of course, the cost is usually off putting, but it more than makes up for it when you have no deflection, no noise, and happy clients.

I agree with Pete - for now, try a spot nail or cleat and see if that secures it. Injection glue may work, and I've done that often in the past, but its not a sure thing and you may need to do it a few times depending on the size of the void underneath. If the subfloor panel is the culprit, injections wont help at all

Another option is trim head screws.

Thanks for help!
I hadn't considered nails, cleats, screws through the top of the board, but it does sound much easier if I can hide it well enough. The type of wood and finish should make hiding these spots much easier, there are already maybe a dozen or so areas that have hidden putty over nails.
Two of these spots span multiple boards so I figure I will need one or two toenails per board? (5" wide planks)
Regarding " the soft grain, the darker part of the grain"
Can you explain this better? I read darker parts of wood are harder summerwood versus softer/lighter springwood. Whats the goal with this placement?

Cleats have a head that can be oriented with the grain of the wood and will blend in easier when fastened into the soft grain of the wood. The soft grain will be the darker part of the grain if the wood is stained, because the softer part will absorb more stain and become darker. As a rule I use colored putty that matches the darker part of the wood color, since light will usually darken or amber the wood over time and will blend in better in the long run.
When the surface is softer the fastener will penetrate the surface easier with less stress which may include spreading the fibers to split in a weak spot even though the wood around the soft spot can be very hard.
Cleats tend to punch through the wood fibers, whereas sharp pointed nails or screws will spread the fibers. Pilot holes take the fibers that interfere with penetration away before the fasteners is driven, either by a hammer, or a screwdriver. A screwdriver can be used to set cleats below the surface
A pilot hole for a cleat will be the diameter of the thickness of the cleat.
A Pilot hole for a nail or screw will be the diameter of the thinest part of the shank with the head diameter as the holding force.