After upgrading to Bootstrap 4.beta.3 i had problems including popper.js. But it turns out Bootstrap has included popper.js since beta.2, see this push request: https://github.com/twbs/bootstrap/pull/23735
If this line in aurelia.json
"main": "js/bootstrap.min.js",
is changed to
"main": "js/bootstrap.bundle.min",
popper.js can be removed from the prepend section and Bootstrap will work.