I can't open .webarchive files made by my own app.

As a temporary solution, you can open the files by setting "allow apps downloaded from" to "Anywhere" in a "Security and Privacy" in a SystemPreferences.

That is to say, the file seems to be treated as apps which  were not code-signed.
I don't know the way to open the files any more.

By the way, when I tried by double-clicking the files, the following allert was displayed.

“hogehoge.webarchive”は壊れているため開けません。 “ゴミ箱”に入れる必要があります。

このファイルは“fugafuga”により今日の 11:21 に作成されました。 

But, I could not open by double-clikking,
I could open the files by choosing a file from a Open menu in Safari, without configuring SystemPreferences.

As your information, in Console.app, I found the following error was logged.

2015/07/27 11:20:16.244 CoreServicesUIAgent[15194]: Error SecAssessmentCreate: 操作を完了できませんでした。（OSStatus エラー -67026）

Here, -67026 was found as an error named errSecCSFileHardQuarantined by referencing OSStatus.com.
http://www.osstatus.com/search/results?platform=all&framework=all&search=-67026

Moreover, you can open files written by Safari by double click.
So, I think it may be OK to open files in a app by which the app made.