Taking individual subjects not related to my career I would like to ask for advice in this particular situation of mine:
I am a Mexican medical doctor, and I am applying for a Master Degree in Biomedical Engineering at a german university. The program offers bridging subjects for students from non-engineering students in the first semester, however, when I e-mailed them about more in-depth information to prepare a more robust application, they told me that mathematics, physics and chemistry subjects are compulsory requisites for this program.

At medical school, I took chemistry and statistics, which may suffice the chemistry and maybe maths with a little bit of imagination, but the physics one eludes me. They specifically required for it to be taught at university so I am struggling a little bit.
As a solution I have tough I may ask for a physics course at my home institution and maybe they will allow me to take it and it may be shown in my transcript (even though I have already finished my career). I don't even know if it is possible to this yet.

I have studied maths and computer science on my own and I have held a chief developer position at a software company for two years now, however, no university is backing up my knowledge on math nor computer science. This at no point does anything for the physics requirement though.

Can anybody offer advice on how could I overcome this complication?
As a faculty member of a German university that also offers a Biomedical Engineering program I can confirm that the admission rules can be quite strict.
However, in almost every study regulation is a clause that the program's examination board (Prüfungsausschuss) can overrule any formal requirement.
The keyword here is "equivalence". E.g., being a software developer can compensate missing software classes, etc. Additional certificates from courses at your home university (as you suggest), even if you take them outside a regular program, can help as well.

So my advice is to bypass the administration and contact directly the head of the program's examination board, or (if such person exists at your target university) the head of the study program (Studiengangsverantwortlicher, sometimes, s/he is the same as the study dean of the program, but not always) and ask what would be needed to prove equivalence.