If the pipe was allowed by you or the prior land owner, then yes a neighbor's pipe can cross your land.
Pipe maintenance is your neighbors responsibility (it is their pipe). And tiding up after repair is also your neighbors responsibility on your property (it is your property), unless you broke the pipe (during construction) then repairs and such are your responsibility. That is theory only. I have found neighbors often do not clean up the messes they create. Your neighbor must also inform you in advance, in writing, if they do maintenance of the pipe on your property.
Providing access to your land for repairs on your neighbors pipe is actually your responsibility. But only to a point of access to repair a pipe. I have seen this limited access rights taken out of context by some neighbors as they think they have more rights then they actually have. It is just a pipe in the ground, not a walk path, access route, area they can pave (actually had a friend who's neighbor came with a back hoe planning to pave my friend's land). So know your rights, and your neighbor's rather limited rights.
You should be able to build over the pipe, but must also still provide your neighbor all necessary access to fix the pipe if needed. And that is where the quandary appears: how to provide access to a pipe under a concrete slab.
Many such pipes are under construction slabs, and should not require direct access for the lifetime of the house so this "technically" should not be a problem. Providing an access cap to "router" out blockage is usually sufficient for routine maintenance. This may require some discussion and negotiation, but a reasonable neighbor when properly informed should usually give the green light to this solution.
In case of excessive demands by a neighbor about your construction over "their" pipe, things can be complicated very quickly. You could also negotiate with your neighbor to just lay a new pipe (if this option exists). Offering to pay for the new pipe on *their* property often does the trick and removes the headache. Some neighbors might be oddly and excessively territorial about their "perceived" "rights" ("rights", that in some cases, only exist in their imagination), so knowing your rights also will be important.
If you have the permits to build a garage, your neighbor can not block your construction. But that does not mean you should just build over the pipe "as is" either. For example, if you want to build a garage and cars will roll over the pipe, if the sewage pipe is of the gray plastic type, then it should be replaced with the red type as only the red type is rated to withstand long term pressure from having a car roll and parked on it. In which case, it may be easier to just relay the pipe so it is not under the garage.