Hi,
If bolts connect the parts that you selected depends (among other things like does the projection of your insertion point hit the part) on the settings for the allowed gap between parts. Also the insertion is working from part to connected part.
THe standard setting for the max gap in management tools is 10mm for the internationla version.

THE 2 plates have a gap of 10 mm in between.
I change the gap to 100. now the parts are not bolted anymore, only one is.

The bolt properties have the setting "finish calculation at gap" which is checked by default. If you uncheck this in this specific sitation, thze bolts connection is no changed, because the gap is always in the direction of the bolt. If You move the bolt to the upper part and uncheck then, the connection gets updated.

So the situations that you most likely have is that some of your connections have a gap below, some above this border.
Try unchecking the setting in your template connection.
HTH,
Christian Blei
Christian Blei
CBT Christian Blei Tools
christianblei.de
youtube.com/channel/UCxjA_NbeScQy9C0Z1xjwXpw