fix: handle duplicated boundary connections in isolate_subsystem

[AayushSabharwal]

Checklist

• Appropriate tests were added
• Any code changes were done in a way that does not break public API
• All documentation related to code changes were updated
• The new code follows the
  contributor guidelines, in particular the SciML Style Guide and
  COLPRAC.
• Any new documentation only uses public API

Additional context

Add any other context about the problem here.

[github-actions]

Benchmark Results (Julia vlts)

Time benchmarks

	master	2c0b79b...	master / 2c0b79b...
ODEProblem	4.15 ± 0.14 ms	4.62 ± 0.47 ms	0.898 ± 0.096
init	0.0686 ± 0.012 ms	0.0705 ± 0.025 ms	0.973 ± 0.38
large_parameter_init/ODEProblem	17.7 ± 4.4 ms	23.1 ± 4.7 ms	0.765 ± 0.25
large_parameter_init/init	0.0782 ± 0.033 ms	0.0722 ± 0.031 ms	1.08 ± 0.65
mtkcompile	7.17 ± 0.39 ms	7.78 ± 0.74 ms	0.921 ± 0.1
sparse_analytical_jacobian/ODEProblem	19.6 ± 1.2 ms	23.8 ± 3 ms	0.824 ± 0.11
sparse_analytical_jacobian/f_iip	0.06 ± 0.01 μs	0.06 ± 0 μs	1 ± 0.17
sparse_analytical_jacobian/f_oop	0.3 ± 0.012 ms	0.299 ± 0.0067 ms	1 ± 0.045
time_to_load	6.8 ± 0.28 s	5.78 ± 0.69 s	1.18 ± 0.15

Memory benchmarks

	master	2c0b79b...	master / 2c0b79b...
ODEProblem	0.0376 M allocs: 1.94 MB	0.0376 M allocs: 1.92 MB	1.01
init	0.417 k allocs: 0.0698 MB	0.417 k allocs: 0.0698 MB	1
large_parameter_init/ODEProblem	0.325 M allocs: 11.4 MB	0.325 M allocs: 11.4 MB	1
large_parameter_init/init	0.605 k allocs: 0.172 MB	0.605 k allocs: 0.172 MB	1
mtkcompile	0.0618 M allocs: 3.45 MB	0.0618 M allocs: 3.43 MB	1
sparse_analytical_jacobian/ODEProblem	0.193 M allocs: 7.93 MB	0.193 M allocs: 7.94 MB	0.998
sparse_analytical_jacobian/f_iip	0 allocs: 0 B	0 allocs: 0 B
sparse_analytical_jacobian/f_oop	0.634 k allocs: 19.6 kB	0.634 k allocs: 19.6 kB	1
time_to_load	0.153 k allocs: 14.6 kB	0.153 k allocs: 14.6 kB	1

[github-actions]

Benchmark Results (Julia v1)

Time benchmarks

	master	2c0b79b...	master / 2c0b79b...
ODEProblem	7.3 ± 1.9 ms	5.51 ± 0.84 ms	1.33 ± 0.4
init	0.0924 ± 0.019 ms	0.0808 ± 0.011 ms	1.14 ± 0.28
large_parameter_init/ODEProblem	0.0348 ± 0.0082 s	0.0366 ± 0.0056 s	0.951 ± 0.27
large_parameter_init/init	0.107 ± 0.041 ms	0.119 ± 0.038 ms	0.898 ± 0.45
mtkcompile	10.5 ± 1.9 ms	8.68 ± 1.4 ms	1.21 ± 0.3
sparse_analytical_jacobian/ODEProblem	0.0338 ± 0.0061 s	28.6 ± 4.9 ms	1.18 ± 0.29
sparse_analytical_jacobian/f_iip	0.08 ± 0.01 μs	0.08 ± 0.01 μs	1 ± 0.18
sparse_analytical_jacobian/f_oop	0.128 ± 0.016 ms	0.131 ± 0.014 ms	0.98 ± 0.16
time_to_load	6.78 ± 0.44 s	7.49 ± 0.71 s	0.905 ± 0.1

Memory benchmarks

	master	2c0b79b...	master / 2c0b79b...
ODEProblem	0.0388 M allocs: 1.99 MB	0.0388 M allocs: 1.97 MB	1.01
init	0.416 k allocs: 0.0518 MB	0.416 k allocs: 0.0518 MB	1
large_parameter_init/ODEProblem	0.352 M allocs: 12.8 MB	0.352 M allocs: 12.8 MB	1
large_parameter_init/init	0.799 k allocs: 0.152 MB	0.799 k allocs: 0.152 MB	1
mtkcompile	0.0598 M allocs: 2.77 MB	0.0598 M allocs: 2.77 MB	1
sparse_analytical_jacobian/ODEProblem	0.186 M allocs: 6.89 MB	0.186 M allocs: 6.89 MB	1
sparse_analytical_jacobian/f_iip	0 allocs: 0 B	0 allocs: 0 B
sparse_analytical_jacobian/f_oop	0.848 k allocs: 27 kB	0.848 k allocs: 27 kB	1
time_to_load	0.146 k allocs: 11.4 kB	0.146 k allocs: 11.4 kB	1