Well, its one of those things that you learn to deal with, but for some reason my tube gets hole on the underside, where it faces the rim, and it happened for the third time in a month... Each time I checked the rim and the tape that covers the spokes - it looks totally fine. Also, I find holes on the underside, but different location each time (relative to the nipple). What could this be? I am using the correctly sized tubes, the tube is 700 35/43, and my tires are 700x38. Maybe I should use different brand tubes?

If you have holes on the rim side, it's likely your rim tape is failing, regardless of how it looks when you remove the tire. Is your rim a double wall rim?
Are you using a cloth tape, rubber strip, or something else for your rim strip?

I am pretty sure its double wall rim, the tape is factory one, looks like some rubberized cloth.

I agree it's probably a rim strip issue.

Are you by chance using those stretchy plastic strips? If so, examine the location of that strip very carefully. If the slightest little arc of a spoke hole in the rim is exposed, your tire air pressure will push your inner tube into that arc and cause it to get cut on the spoke hole edge.

Are the holes in the center where the spoke nipples are, or our at the rim edge? If they are at the edge of the rim it could be a pinch flat, but typically it will happen at both edges and look like a snake bite (two holes). If this is the case you may be running your tire pressure too low.
If they are at the centre then disregard what I have said.

Replace the rim strip or tape. I you have nothing else handy, black electrical tape works in a pinch, but apply it over the top of your existing rim strip or tape.

https://www.schwalbetires.com/access...m_tape_singles

Was the hole visible?
Could it be just a bad tube? My niece called yesterday, wanted to go for bike ride on her new (bought last fall) bike. She had noticed a tire flat several weeks ago, took it in to the place where she bought it. They said it was fine aired it up and she took it home. A few weeks later now, tire flat again.
She brought the bike over, took off the wheel, put about 70# in it, submerged it and found tiny bubbles emerging from beneath the rim at one place. Marked that, took the tire off and inspected the tube there. Nothing at all visible. Tried submerging the tube but couldn't inflate it enough to cause the suspect area to stretch, what I think is defective material, to recreate the leak.
Out tire sizes are the same, but mine use Presta valves her's are Schrader. They had given her a small tire repair kit at purchase, that contained a spare tube. Installed that and she was on her way. I'm a little skeptical since I couldn't replicate the problem. So, since her backup tube is the same brand (Kenda) can't be sure her problem is solved.

I never came across a tube I couldn't inflate enough to find a hole if there is one. You can inflate it to much larger than the deflated tube without damaging it. Have you checked for a slow leak at the valve If it is deflating over a couple of weeks, the hole may be very small or the valve could be leaking a bit.

As to the OP. Do you mean the holes in the tube are at different places relative to the valve opening in the rim? If that is the case it is more of a mystery. If the cause was a bad point in the rim liner the hole should always be at one point on the tube equidistant from the valve. In a pinch you can cover the existing liner with narrow electrical tape. I've done that for years and it works fine.
Have you run your hand around the inside of the rim looking for burrs? It's easy to file down them if you find one. That could be your source of the holes but it still would be located around the same distance from the valve on all of the tubes.

Butyl rim strips or strips that aren't tight enough to prevent movement or sliding on the rim can be pushed out of position by unmounting and remounting the tire to patch the leak. I ended up with two flats on a tour once. One from a glass shard, and one miles later from an exposed spoke hole. If the strip needs to be replaced, it's possible to expose new spoke holes to cut the tube.

When i have a tube that won't hold enough air to let me search for the hole (or holes, usually) I either fold, clamp, or tie the tube into segments. That way i can localize the hole---and often, I can work my way around the tube, folding over a section and inflating the rest, then folding over the next section, until I have narrowed down the hole's location pretty well. Then I fold that section, clamp it (with anything---two small pieces of wood and a vice grip?) and get the rest of the tube really puffed up. So far, every time, I have been able to slowly open up the clamped part and find the holes----and by every time, I mean, 'in more than fifty years of doing this" so I at least, have faith in the method.

I figured it must be bad/cheap rim tape, so I ordered beefy Velox cotton rim tape. I just got it. Do I tape it over the flimsy rubber rim tape that is already there, or take it off first? I never put my own rim tape in place, any tips?

Remove the old rim strip, clean the rim bed, and line up the valve stem holes. I overlap the tape ends a little, maybe 3cm.

Narrow tape for wide rims, wide tape for narrow rims. This sounds bass-ackwards but it's because wide rims have a center trough that's narrower than narrow rims. The concern is to completely cover all the spoke holes, not the entire rim bed. You only want one layer of rim strip; just make sure it's an effective layer! You might also want to examine the rim for a rough spot somewhere else on the inside, not just at a hole.

It's not valid to submerge the wheel - tire, rim, and all - and determine where the hole is. Air will leak out of any random spoke hole. And if the hole so big it's preventing you from inflating the tube, then its location should be obvious. Pump while someone else visually examines the tube more closely.

Thank you guys, I have replaced the rim tape. The thick cotton 22mm Velox tape nicely filled the rim wall to wall. The thin and narrow flimsy plastic band that was there before was a total joke in comparison. Hopefully this will put a stop to tube failures on the side facing the rim.

If you have trouble mounting the tire, the thicker tape can sometimes be to blame. For me, I'll use the thinner strip wall to wall, and the thicker tape just to cover the spoke holes/ heads of the nipples (for vintage single wall rims).

Happy trails!

Yes, the tire did have a pretty snug fit, I noticed. The tape was thick and taking the entire width of the rim. But it looked like a very reliable set up, so I am going to stick to this arrangement.

I finally switched to tubeless and haven’t had a flat since.

most likely rim strip issue