You don't mention the type of bicycle you're referring to, but if you look at your wheels with the tube out and the tires off, you can probably see what the root cause is.
Bicycle wheels should have rim tape or a rim strip that protects the tube from the spoke holes in the rim. Of the two approaches, the rim strip is the more modern. The rim strip can be rubber, or plastic, or a slightly stretchable woven material (polyester fabric, for example).
Usually if you have an undamaged rim strip of the correct size for your wheel, it is highly unlikely that your tube is being punctured by contact with the spoke holes/spoke nipples. It might be cut by the hole where the valve stem goes through the rim, but if so it should be obvious.
However if you have rim tape, even if it is the correct width, it's possible the rim tape is not adhering to the rim in one or more locations, and could be moving around under the tube, thus exposing the spoke holes, and causing your tubes to pop.
The leak you describe-- taking a few minutes to become flat-- suggests a small hole, and this is not inconsistent with a tube cut by a spoke hole, but usually such a cut is big enough to let the air out almost immediately.
To find out, inspect your leaky tube. Remove it from the wheel, and pump a bit of air into it. Where is the hole? If it is on the valve side of the tube-- the portion which comes into contact with rim tape/rim strip/spoke holes-- then this may be your problem. Hold the tube under water, if necessary, to see where bubbles emerge.
If the hole is on the outside of the tube, where the tube is in contact with your tire, you need to check the tire carefully. One might expect the bike shop did this, but you never know. Run your fingers over the inside of the tire. As the other responder suggested, you can get a small hole from a piece of wire (a "michelin thorn") that has punctured your tire casing, or a goat-head thorn, or a piece of glass. You need to remove that from the tire casing, or it will puncture every new tube you put in.