1. Excessive schedule pressure:
The Vasa was launched with an aggressive schedule that did not allow the shipbuilders to adequately redesign the ship to accommodate modifications requested by the king. Likewise the space shuttle fleet was plagued by schedule pressure throughout its history, with Congress repeatedly turning up the pressure on NASA to establish an operational shuttle fleet.
2. Changing needs:
The Vasa was originally designed to be a 108 foot ship, but was completed as a 135 foot vessel. Likewise, the Shuttle, originally was designed as a relatively small spaceplane that would sit on top of the booster stack. Additional scientific and military requirements cause the space shuttle to be scaled up into a much larger system that would sit alongside the boosters. In addition, these changing requirements ensured that testing was conducted on an accelerated schedule, further adding risk to the project.
3. Lack of technical specifications:
This is one place where the Vasa and shuttle narratives diverge. NASA was very diligent about ensuring that technical specifications were up to date and that changes were propagated to the appropriate working groups in a timely manner. These detailed changes and documentation were instrumental in conducting post-disaster analysis.
4. Lack of documented project plan:
The Vasa did not have a documented project plan, or if it did, it didn't survive into the present day. The Shuttle did have a very well documented project plan, but there were so many changes, few knew what the overall plan was, so the effect was remarkably like not having a plan at all. Unlike with technical specifications, mid-level managers and low-level NASA engineers often did not have a good understanding of what the current "big picture" status was with the Shuttle design.
5. Excessive innovation:
The Vasa attempted to incorporate a second gun deck, whilst simultaneously attempting to set a size record for the shipyard and the country. The Shuttle incorporated numerous innovations: reusable heat shields, innovative liquid-fueled motors, new electronic flight control systems. These innovations (particularly the heat shield and the liquid fueled motors) were significant timesinks and drew time and manpower away from other parts of the project that were considered "safe" (in this case, the reusable solid rocket boosters). Likewise, it appears that the shipwrights of the Vasa had so many other concerns, they didn't have time to pay attention to basic seaworthiness concerns.
6. Secondary innovations
This is closely related to the point above. Just like the Vasa required additional innovations to accommodate her second gundeck, the Space Shuttles required numerous secondary innovations to accommodate the new technologies that they were to incorporate. In both the space shuttle disasters, the final, fatal flaw was in a secondary innovation.
In the case of Challenger, the zinc oxide putty that was sealing the gaps between segments of the solid rocket boosters failed, allowing rocket gases to attack and burn holes through the O-rings. In the case of Columbia, the carbon-carbon panels that were shattered by falling ice were there to protect the leading edges of the wings - the original shuttle design didn't have such panels, as the original shuttle design called for the use of heat-resistant titanium alloy.
7. Requirements creep
The Vasa evolved significantly over it's 2.5 years of construction. The space shuttle evolved even more. It went from a relatively modest astronaut transport system to the be-all end-all space launch system for NASA. That, combined with schedule pressure, ensured that there were outstanding design issues when the system was put into production.
8. Lack of scientific methods
Here again, the two narratives diverge. Unlike 16th century shipbuilders, 1970s NASA was highly experienced in designing and building rockets. What sank the shuttle was not lack of scientific measurement and method, but a process of normalization of deviance, where increasingly deviant measurements were redefined as "normal" by virtue of the fact that in this instance nothing untoward resulted from the abnormal parameter.
9. Ignoring the obvious
The Vasa was launched after failing a rudimentary stability test. The space shuttle exhibited hot-gas impingement on it's O-rings on the second test flight. However, in both cases, the solution was to apply a patch and move on as if the problem had been solved. For the Vasa, it was additional ballast. For the shuttle, it was a series of tweaks to putty composition and application technique. In both cases, the tweaks did not fix the underlying problem, and were well-intended best efforts to fix design issues after the system had been built.
10. Possible mendacity
While the Congressional report does indicate mendacity on the part of NASA middle managers, Vaughan's account absolves these managers of mendacity. She says that the Congressional report misinterpreted internal NASA terms (like "waiver", for example) whose meanings had diverged from their common-language usage.
Despite a few points of divergence, it's striking how parallel the courses of the Vasa and the Challenger are. Both were groundbreaking, innovative flagships and symbols of national pride. Both were designed and built under intense schedule pressure and fluctuating requirements. And finally, both met tragic fates due to fundamental flaws in their design. Our knowledge of scientific principles may have improved over the past three hundred years, but our knowledge of sound project management techniques sure hasn't.
This applies everywhere. Without a culture that encourages everyone at every position of power to be honest and express their true opinions then you just end up with a system built on deception and false beliefs.