That's more an indication that their farm was thin than anything else. Him jumping over Margot isn't shocking either. Margot's season up to the mid season update where he was ranked 24th was pretty solid with a .755 OPS (.328 OBP), stellar defense and 25 steals in 61 games (.409 per game). After that update he had a .730 OPS and 15 stolen bases over 49 games (.29 per game). He then posted a .639 OPS with 1 steal over 15 Dominican Winter League games. His star is currently dimming.Look at how BA rated the Padres top 10 prospects. Guerra is #1.
http://www.baseballamerica.com/minors/san-diego-padres-top-10-prospects/