That's not wrong ...
Yes it is.
Programs include but is not limited to autosofts, activesofts, knowsofts, linguasofts, common cyberprograms, hacking cyberprograms, agents, mapsofts, shopsofts and tutorsofts.
If they are not cyberprograms (which they probably should be) then it would be legal to run them in a commlink or a skilljack (and there are several threads about people asking about running them in commlinks so obviously it is easy to miss that they are actually special cyberprograms and not a regular program like a mapsoft). As you also noted it give the ambiguous impression that you might or might not use virtual machine to run autosofts.
- and it also raise the question if you might or might not use virtual machine to run agents...
If the whole chapter used the word cyberprograms instead of programs but virtual machine used the word programs then it would be clear that you can use it to run multiple autosofts and agents. It virtual machine instead used the phrase "cyberprograms and agents" it would be clear that you can not use it to run autosofts. Currently they use the word "programs" in the whole chapter and by context they mean cyberprograms and maybe agents. This mean virtual machine can be used for cyberprograms, it might be used for agents and it can probably not be used for autosofts - but everything is guesswork and it is impossible to figure out the correct intent by just reading the text.
Everything simply get less confusing and a lot easier to understand if you use the correct words and phrases at all times.
"Common programs" is at best ambiguous and at worst not correct at all.
"Common cyberprograms" or "Cyberprograms, common use" is correct (and they even use this phrase in the table on p.442).