Do the Neolutionists really own the clones and Kira?
No, that's not the way that genomic patents work. First and foremost, human beings are not property, no matter how they're made. The guy who holds the patent on in-vitro fertilization doesn't own the children who were conceived that way. An AgriCorp may own the genomic patents on the seeds they produce but the farmer still owns the wheat they grow. Genomic patents apply to an intellectual property that's used to develop technologies, not the end-product of using those technologies. Of course, since the Neolutionists aren't really concerned with moral or ethical niceties they're probably not planning on taking things into a court of law.
Or the patent was put in place in preparation for a time when they gain enough influence to change the laws, allowing them to conduct their experiments legally and legally own the clones.
The sentence encoded in he clones' DNA is not a patent, despite what Cosima says. It's a statement of property. In any case, not enforceable legally, since cloning is illegal. There's also the question of whether a clone can be property, which could be disputed if cloning becomes legal.
If Maggie Chen was 41 and the clones are about 29 (according to their passports), how is it possible that Maggie helped make them, like Helena said? Maggie would have been something like 12 when they were born, and even younger when the science was happening.
Its possible that Helena was lied to or doesn't really know what's going on.
Why didn't Beth find Sarah when she searched the Europeans' photos for matches on the police database? Especially considering that Sarah has a criminal record.
Sarah was moved to Canada when she was still a minor. Her criminal record is Canadian.