If you could, please go open this ticket over on mybatis-3 core and work with me to figure this issue out. I'm switching from maven bundle plugin to bnd-maven-plugin basically now and will want you to test out if that makes any differences then we can go from there. We have osgi basically built into our parent pom for years and its not changed much in my time and I don't use OSGI to know much about it. For javassist we are shading that but personally I think we should not be doing such things these days. At any rate, unlike normal go to user group, please take discussion over to an issue at the core here
https://github.com/mybatis/mybatis-3/issues. Regardless if this is an user related issue or simply something we have wrong for a long time, it will be greatly beneficial to have an osgi user help confirm our transition of the plugin and fix up any loose ends.