one of the basic examples is the description of wave function whci is backbone of QM, where in many books they represent it with a plane wave solution, which is not square integrable and provides constant probability for a particle everywhere...
As regards your particular example of plane waves: as you’re probably aware, a square-integrable 3D wave packet can be constructed via a linear combination (superposition) of plane waves, so I think the mention of plane waves is really just a pedagogic point, to illustrate the uncertainty principle in terms of “particle” with a constant distribution through (1D) space. Someone has outlined the plane wave issue in the attached link.
As for good books for the undergraduate level (and therefore unlikely to be free of all the misconceptions you’re concerned about), I’ll assume you’re talking about physics and chemistry undergrads (rather than books for non-specialists and liberal arts courses):
Of the more recent ones:
- David J. Griffiths "Introduction to Quantum Mechanics” (2nd ed) is the one most frequently recommended these days
- David A. B. Miller "Quantum Mechanics for Scientists and Engineers" is another I like, for it’s ‘grounded’ (i.e. none-too-abstract) approach
- Davies and Betts “Quantum Mechanics” is short and snappy.
Earlier ones, highly recommended e.g. on Amazon (may be out of print, but often there are PDF copies that can easily be found on the internet)
- Feynman, Leighton & Sands, Lectures in Physics, Vol III (needs no introduction)
- Dicke & Wittke "Introduction to Quantum Mechanics” (and out of print, though a PDF of it can be found on the internet) is strongly recommended; and see Ch 2 for the plane wave issue, p. 23 in my copy.
- P.T. Matthews "Introduction to Quantum Mechanics” (2nd ed) Short but gets right to the heart of the usual basics (high price on Amazon, unfortunately)
What are some of the other misconceptions you're concerned about?