Potential formatting issues in some sample_examples entries

[barabbs]

Hi,

I see that problem_3 and problem_5 in sample examples are missing the generated_spec_body tags, having both the statement and the body of the generated specifications wrapped in the generated_spec sections.

Also in problem_1 there's a additional by keyword at the end of the spec_isomorphism section, inconsistent with all other entries.

I will submit a PR shortly addressing this.